Starting phenix.real_space_refine on Fri Sep 11 00:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dd3_30643/09_2026/7dd3_30643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd3_30643/09_2026/7dd3_30643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dd3_30643/09_2026/7dd3_30643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd3_30643/09_2026/7dd3_30643.map" model { file = "/net/cci-nas-00/data/ceres_data/7dd3_30643/09_2026/7dd3_30643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd3_30643/09_2026/7dd3_30643.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dd3_30643/09_2026/7dd3_30643.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dd3_30643/09_2026/7dd3_30643.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 9 5.49 5 S 34 5.16 5 C 3756 2.51 5 N 1000 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5929 Number of models: 1 Model: "" Number of chains: 3 Chain: "x" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5193 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 619} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "y" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 164 Classifications: {'RNAv2': 9} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 5} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.58, per 1000 atoms: 0.27 Number of scatterers: 5929 At special positions: 0 Unit cell: (145.22, 115.54, 86.92, 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) S 34 16.00 P 9 15.00 O 1130 8.00 N 1000 7.00 C 3756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 286.3 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 47.0% alpha, 11.0% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'x' and resid 215 through 221 removed outlier: 3.988A pdb=" N LYS x 221 " --> pdb=" O GLN x 217 " (cutoff:3.500A) Processing helix chain 'x' and resid 223 through 227 removed outlier: 3.533A pdb=" N GLN x 227 " --> pdb=" O PRO x 224 " (cutoff:3.500A) Processing helix chain 'x' and resid 228 through 239 removed outlier: 4.254A pdb=" N GLN x 234 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing helix chain 'x' and resid 254 through 264 removed outlier: 4.218A pdb=" N GLN x 258 " --> pdb=" O THR x 254 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU x 260 " --> pdb=" O LEU x 256 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL x 261 " --> pdb=" O PRO x 257 " (cutoff:3.500A) Processing helix chain 'x' and resid 279 through 294 removed outlier: 3.552A pdb=" N THR x 284 " --> pdb=" O ARG x 280 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG x 289 " --> pdb=" O SER x 285 " (cutoff:3.500A) Processing helix chain 'x' and resid 323 through 334 removed outlier: 3.654A pdb=" N LEU x 327 " --> pdb=" O THR x 323 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU x 328 " --> pdb=" O ASP x 324 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG x 329 " --> pdb=" O GLY x 325 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE x 331 " --> pdb=" O LEU x 327 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU x 332 " --> pdb=" O LEU x 328 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR x 333 " --> pdb=" O ARG x 329 " (cutoff:3.500A) Processing helix chain 'x' and resid 352 through 369 removed outlier: 4.135A pdb=" N ASP x 364 " --> pdb=" O GLY x 360 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU x 366 " --> pdb=" O LEU x 362 " (cutoff:3.500A) Proline residue: x 367 - end of helix Processing helix chain 'x' and resid 382 through 390 removed outlier: 3.799A pdb=" N PHE x 386 " --> pdb=" O ASN x 382 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER x 387 " --> pdb=" O ALA x 383 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU x 388 " --> pdb=" O LYS x 384 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE x 389 " --> pdb=" O LYS x 385 " (cutoff:3.500A) Processing helix chain 'x' and resid 416 through 432 removed outlier: 3.534A pdb=" N ALA x 420 " --> pdb=" O ASN x 416 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE x 426 " --> pdb=" O ILE x 422 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR x 431 " --> pdb=" O GLN x 427 " (cutoff:3.500A) Processing helix chain 'x' and resid 445 through 462 removed outlier: 3.806A pdb=" N THR x 451 " --> pdb=" O GLU x 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE x 458 " --> pdb=" O LYS x 454 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER x 460 " --> pdb=" O GLU x 456 " (cutoff:3.500A) Processing helix chain 'x' and resid 479 through 484 Processing helix chain 'x' and resid 542 through 551 Processing helix chain 'x' and resid 566 through 573 Processing helix chain 'x' and resid 580 through 585 removed outlier: 3.565A pdb=" N ARG x 584 " --> pdb=" O PRO x 580 " (cutoff:3.500A) Processing helix chain 'x' and resid 589 through 597 Processing helix chain 'x' and resid 612 through 626 removed outlier: 3.654A pdb=" N SER x 619 " --> pdb=" O THR x 615 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU x 620 " --> pdb=" O LEU x 616 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU x 626 " --> pdb=" O ASN x 622 " (cutoff:3.500A) Processing helix chain 'x' and resid 636 through 645 removed outlier: 3.694A pdb=" N MET x 641 " --> pdb=" O ARG x 637 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS x 643 " --> pdb=" O GLY x 639 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU x 644 " --> pdb=" O LYS x 640 " (cutoff:3.500A) Processing helix chain 'x' and resid 650 through 658 removed outlier: 3.604A pdb=" N VAL x 654 " --> pdb=" O GLU x 650 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR x 656 " --> pdb=" O ALA x 652 " (cutoff:3.500A) Processing helix chain 'x' and resid 667 through 679 removed outlier: 4.164A pdb=" N THR x 673 " --> pdb=" O GLU x 669 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS x 679 " --> pdb=" O VAL x 675 " (cutoff:3.500A) Processing helix chain 'x' and resid 688 through 697 removed outlier: 3.725A pdb=" N ALA x 692 " --> pdb=" O GLN x 688 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER x 695 " --> pdb=" O ASP x 691 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL x 696 " --> pdb=" O ALA x 692 " (cutoff:3.500A) Processing helix chain 'x' and resid 704 through 716 Processing helix chain 'x' and resid 721 through 727 removed outlier: 3.710A pdb=" N GLN x 725 " --> pdb=" O ARG x 721 " (cutoff:3.500A) Processing helix chain 'x' and resid 730 through 751 Processing helix chain 'x' and resid 752 through 763 removed outlier: 3.782A pdb=" N LYS x 756 " --> pdb=" O GLY x 752 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN x 759 " --> pdb=" O GLU x 755 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA x 760 " --> pdb=" O LYS x 756 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG x 761 " --> pdb=" O ASN x 757 " (cutoff:3.500A) Processing helix chain 'x' and resid 770 through 783 removed outlier: 3.889A pdb=" N THR x 776 " --> pdb=" O ASN x 772 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG x 777 " --> pdb=" O ALA x 773 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER x 781 " --> pdb=" O ARG x 777 " (cutoff:3.500A) Processing helix chain 'x' and resid 813 through 821 removed outlier: 3.563A pdb=" N HIS x 819 " --> pdb=" O LEU x 815 " (cutoff:3.500A) Processing helix chain 'x' and resid 852 through 859 removed outlier: 4.129A pdb=" N ILE x 856 " --> pdb=" O GLU x 852 " (cutoff:3.500A) Processing helix chain 'x' and resid 859 through 867 removed outlier: 6.378A pdb=" N ASP x 865 " --> pdb=" O GLN x 861 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU x 866 " --> pdb=" O ILE x 862 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE x 867 " --> pdb=" O PHE x 863 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 14 Processing helix chain 'y' and resid 93 through 100 removed outlier: 3.865A pdb=" N TYR y 97 " --> pdb=" O THR y 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN y 98 " --> pdb=" O GLU y 94 " (cutoff:3.500A) Processing helix chain 'y' and resid 101 through 112 removed outlier: 4.142A pdb=" N GLY y 106 " --> pdb=" O VAL y 102 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP y 107 " --> pdb=" O GLU y 103 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU y 110 " --> pdb=" O GLY y 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 310 through 311 removed outlier: 7.443A pdb=" N GLN x 272 " --> pdb=" O CYS x 342 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N MET x 344 " --> pdb=" O GLN x 272 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA x 274 " --> pdb=" O MET x 344 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER x 341 " --> pdb=" O LYS x 373 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU x 375 " --> pdb=" O SER x 341 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE x 343 " --> pdb=" O LEU x 375 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER x 377 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE x 345 " --> pdb=" O SER x 377 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE x 396 " --> pdb=" O VAL x 241 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE x 243 " --> pdb=" O PHE x 396 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL x 398 " --> pdb=" O ILE x 243 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N MET x 245 " --> pdb=" O VAL x 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 406 through 409 removed outlier: 6.267A pdb=" N ASP x 437 " --> pdb=" O TYR x 515 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE x 517 " --> pdb=" O ASP x 437 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU x 439 " --> pdb=" O ILE x 517 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE x 438 " --> pdb=" O VAL x 498 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA x 500 " --> pdb=" O ILE x 438 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL x 440 " --> pdb=" O ALA x 500 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN x 468 " --> pdb=" O ARG x 495 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL x 497 " --> pdb=" O GLN x 468 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE x 470 " --> pdb=" O VAL x 497 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU x 499 " --> pdb=" O ILE x 470 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR x 472 " --> pdb=" O LEU x 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 521 through 528 Processing sheet with id=AA4, first strand: chain 'x' and resid 795 through 797 removed outlier: 3.690A pdb=" N VAL x 830 " --> pdb=" O VAL x 788 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR x 829 " --> pdb=" O ILE x 849 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'x' and resid 808 through 809 removed outlier: 6.803A pdb=" N SER x 808 " --> pdb=" O ILE x 843 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 190 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.60 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: 1616 1.33 - 1.45: 928 1.45 - 1.57: 3429 1.57 - 1.69: 18 1.69 - 1.80: 55 Bond restraints: 6046 Sorted by residual: bond pdb=" N THR y 93 " pdb=" CA THR y 93 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.75e+00 bond pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta sigma weight residual 1.530 1.573 -0.043 1.69e-02 3.50e+03 6.48e+00 bond pdb=" CG LEU x 835 " pdb=" CD1 LEU x 835 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.60e+00 bond pdb=" CB VAL x 788 " pdb=" CG2 VAL x 788 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.48e+00 bond pdb=" CG LEU x 831 " pdb=" CD2 LEU x 831 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.18e+00 ... (remaining 6041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 7660 2.02 - 4.03: 442 4.03 - 6.05: 75 6.05 - 8.07: 12 8.07 - 10.09: 6 Bond angle restraints: 8195 Sorted by residual: angle pdb=" C LYS x 300 " pdb=" N GLU x 301 " pdb=" CA GLU x 301 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N THR x 681 " pdb=" CA THR x 681 " pdb=" C THR x 681 " ideal model delta sigma weight residual 109.81 118.85 -9.04 2.21e+00 2.05e-01 1.67e+01 angle pdb=" N ILE x 273 " pdb=" CA ILE x 273 " pdb=" C ILE x 273 " ideal model delta sigma weight residual 109.21 114.59 -5.38 1.36e+00 5.41e-01 1.56e+01 angle pdb=" CB MET x 322 " pdb=" CG MET x 322 " pdb=" SD MET x 322 " ideal model delta sigma weight residual 112.70 102.61 10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N THR y 93 " pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta sigma weight residual 110.49 116.11 -5.62 1.69e+00 3.50e-01 1.11e+01 ... (remaining 8190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 3458 16.59 - 33.19: 166 33.19 - 49.78: 63 49.78 - 66.37: 20 66.37 - 82.96: 5 Dihedral angle restraints: 3712 sinusoidal: 1603 harmonic: 2109 Sorted by residual: dihedral pdb=" C4' U G 530 " pdb=" C3' U G 530 " pdb=" C2' U G 530 " pdb=" C1' U G 530 " ideal model delta sinusoidal sigma weight residual 36.34 -37.85 74.19 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4' U G 528 " pdb=" C3' U G 528 " pdb=" C2' U G 528 " pdb=" C1' U G 528 " ideal model delta sinusoidal sigma weight residual 36.35 -35.71 72.06 1 3.10e+00 1.04e-01 6.91e+02 dihedral pdb=" C4' U G 529 " pdb=" C3' U G 529 " pdb=" C2' U G 529 " pdb=" C1' U G 529 " ideal model delta sinusoidal sigma weight residual 36.34 -33.33 69.67 1 3.10e+00 1.04e-01 6.52e+02 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 726 0.074 - 0.148: 202 0.148 - 0.222: 21 0.222 - 0.296: 10 0.296 - 0.370: 2 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA THR y 93 " pdb=" N THR y 93 " pdb=" C THR y 93 " pdb=" CB THR y 93 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB ILE x 843 " pdb=" CA ILE x 843 " pdb=" CG1 ILE x 843 " pdb=" CG2 ILE x 843 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C3' U G 530 " pdb=" C4' U G 530 " pdb=" O3' U G 530 " pdb=" C2' U G 530 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 958 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE x 783 " -0.008 2.00e-02 2.50e+03 2.02e-02 7.17e+00 pdb=" CG PHE x 783 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE x 783 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE x 783 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE x 783 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE x 783 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE x 783 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU x 223 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO x 224 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO x 224 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO x 224 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS x 810 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO x 811 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO x 811 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO x 811 " -0.030 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1995 2.87 - 3.37: 5326 3.37 - 3.88: 9135 3.88 - 4.39: 10580 4.39 - 4.90: 17919 Nonbonded interactions: 44955 Sorted by model distance: nonbonded pdb=" OE1 GLN x 305 " pdb=" NZ LYS x 320 " model vdw 2.357 3.120 nonbonded pdb=" O LEU x 337 " pdb=" NH1 ARG x 369 " model vdw 2.362 3.120 nonbonded pdb=" O LEU x 508 " pdb=" NH2 ARG x 552 " model vdw 2.363 3.120 nonbonded pdb=" O ALA x 420 " pdb=" OG1 THR x 424 " model vdw 2.399 3.040 nonbonded pdb=" NZ LYS x 363 " pdb=" O PHE x 389 " model vdw 2.411 3.120 ... (remaining 44950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.012 0.080 6046 Z= 0.475 Angle : 1.079 10.087 8195 Z= 0.564 Chirality : 0.070 0.370 961 Planarity : 0.008 0.055 1008 Dihedral : 12.659 82.961 2344 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.32 % Favored : 94.54 % Rotamer: Outliers : 2.31 % Allowed : 4.01 % Favored : 93.68 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.26), residues: 714 helix: -3.83 (0.15), residues: 269 sheet: -1.38 (0.46), residues: 122 loop : -1.52 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG x 844 TYR 0.033 0.004 TYR x 795 PHE 0.039 0.004 PHE x 783 TRP 0.026 0.004 TRP x 568 HIS 0.009 0.002 HIS y 142 Details of bonding type rmsd/Z covalent geometry : bond 0.01168 / 0.48 ( 6046) covalent geometry : angle 1.07943 / 0.56 ( 8195) hydrogen bonds : bond 0.32991 / 20.91 ( 190) hydrogen bonds : angle 9.21972 / 6.39 ( 558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 256 LEU cc_start: 0.8840 (mm) cc_final: 0.8451 (mm) REVERT: x 272 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7245 (pt0) REVERT: x 488 GLN cc_start: 0.8230 (mt0) cc_final: 0.7638 (pp30) REVERT: x 758 ASP cc_start: 0.7587 (m-30) cc_final: 0.7277 (m-30) REVERT: x 796 GLN cc_start: 0.8135 (mt0) cc_final: 0.7810 (pt0) REVERT: y 109 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8651 (tm) outliers start: 15 outliers final: 4 residues processed: 173 average time/residue: 0.0965 time to fit residues: 21.1644 Evaluate side-chains 100 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 268 GLN Chi-restraints excluded: chain x residue 271 LEU Chi-restraints excluded: chain x residue 272 GLN Chi-restraints excluded: chain x residue 837 LEU Chi-restraints excluded: chain y residue 90 GLU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 239 ASN x 382 ASN x 412 GLN x 419 HIS x 427 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118593 restraints weight = 7304.380| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.96 r_work: 0.3319 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6046 Z= 0.150 Angle : 0.859 16.552 8195 Z= 0.381 Chirality : 0.066 0.942 961 Planarity : 0.005 0.042 1008 Dihedral : 9.612 122.301 887 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.93 % Allowed : 8.94 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.29), residues: 714 helix: -1.65 (0.25), residues: 306 sheet: -0.32 (0.54), residues: 96 loop : -1.47 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG x 289 TYR 0.029 0.002 TYR x 304 PHE 0.012 0.001 PHE x 863 TRP 0.011 0.001 TRP x 568 HIS 0.007 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6046) covalent geometry : angle 0.85895 / 0.38 ( 8195) hydrogen bonds : bond 0.04412 / 2.86 ( 190) hydrogen bonds : angle 4.96086 / 3.50 ( 558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: x 256 LEU cc_start: 0.8986 (mm) cc_final: 0.8426 (mm) REVERT: x 265 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7287 (t80) REVERT: x 304 TYR cc_start: 0.7650 (p90) cc_final: 0.7394 (p90) REVERT: x 309 GLU cc_start: 0.6912 (mp0) cc_final: 0.6475 (tp30) REVERT: x 346 ASP cc_start: 0.8495 (t0) cc_final: 0.8058 (t0) REVERT: x 373 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7710 (mptt) REVERT: x 488 GLN cc_start: 0.8498 (mt0) cc_final: 0.7830 (pp30) REVERT: x 721 ARG cc_start: 0.8916 (ttm-80) cc_final: 0.8475 (ttt90) REVERT: x 725 GLN cc_start: 0.8682 (mt0) cc_final: 0.8028 (mt0) REVERT: x 758 ASP cc_start: 0.8176 (m-30) cc_final: 0.7870 (m-30) REVERT: x 796 GLN cc_start: 0.8167 (mt0) cc_final: 0.7370 (pt0) REVERT: x 851 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7661 (mttm) REVERT: y 90 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: y 109 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8170 (tm) outliers start: 19 outliers final: 6 residues processed: 129 average time/residue: 0.0762 time to fit residues: 13.1502 Evaluate side-chains 104 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 332 LEU Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 836 MET Chi-restraints excluded: chain x residue 837 LEU Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 90 GLU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 258 GLN x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.166136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117678 restraints weight = 7266.797| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.96 r_work: 0.3303 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6046 Z= 0.142 Angle : 0.725 11.912 8195 Z= 0.326 Chirality : 0.057 0.677 961 Planarity : 0.004 0.037 1008 Dihedral : 9.373 159.602 879 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.24 % Allowed : 10.48 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.31), residues: 714 helix: -0.64 (0.28), residues: 307 sheet: 0.02 (0.56), residues: 96 loop : -1.16 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG x 307 TYR 0.028 0.002 TYR x 304 PHE 0.018 0.001 PHE x 565 TRP 0.006 0.001 TRP x 568 HIS 0.004 0.001 HIS x 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6046) covalent geometry : angle 0.72468 / 0.33 ( 8195) hydrogen bonds : bond 0.03924 / 2.49 ( 190) hydrogen bonds : angle 4.38711 / 3.11 ( 558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7832 (ttm) cc_final: 0.6801 (mmt) REVERT: x 265 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7299 (t80) REVERT: x 304 TYR cc_start: 0.7895 (p90) cc_final: 0.7611 (p90) REVERT: x 309 GLU cc_start: 0.6941 (mp0) cc_final: 0.6548 (tp30) REVERT: x 346 ASP cc_start: 0.8547 (t0) cc_final: 0.8335 (t0) REVERT: x 373 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7619 (mptt) REVERT: x 402 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: x 488 GLN cc_start: 0.8482 (mt0) cc_final: 0.7894 (pp30) REVERT: x 690 ARG cc_start: 0.8354 (tmm-80) cc_final: 0.8133 (tmm-80) REVERT: x 720 SER cc_start: 0.8919 (t) cc_final: 0.8685 (p) REVERT: x 725 GLN cc_start: 0.8749 (mt0) cc_final: 0.8422 (mp10) REVERT: x 758 ASP cc_start: 0.8081 (m-30) cc_final: 0.7641 (m-30) REVERT: x 762 MET cc_start: 0.7518 (mmp) cc_final: 0.7296 (mmp) REVERT: x 796 GLN cc_start: 0.8202 (mt0) cc_final: 0.7439 (pt0) REVERT: x 851 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7746 (mttm) REVERT: y 109 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8197 (tm) outliers start: 21 outliers final: 10 residues processed: 122 average time/residue: 0.0787 time to fit residues: 12.7868 Evaluate side-chains 108 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 332 LEU Chi-restraints excluded: chain x residue 338 SER Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 836 MET Chi-restraints excluded: chain x residue 837 LEU Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 96 GLU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.163964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116105 restraints weight = 7298.145| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.92 r_work: 0.3291 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6046 Z= 0.163 Angle : 0.689 10.936 8195 Z= 0.316 Chirality : 0.055 0.489 961 Planarity : 0.004 0.035 1008 Dihedral : 9.160 163.464 876 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 3.54 % Allowed : 12.63 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.31), residues: 714 helix: -0.24 (0.29), residues: 309 sheet: 0.05 (0.56), residues: 96 loop : -1.05 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 289 TYR 0.024 0.002 TYR x 304 PHE 0.017 0.001 PHE x 565 TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 6046) covalent geometry : angle 0.68886 / 0.32 ( 8195) hydrogen bonds : bond 0.03784 / 2.40 ( 190) hydrogen bonds : angle 4.22170 / 3.02 ( 558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7900 (ttm) cc_final: 0.7244 (mmt) REVERT: x 265 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7333 (t80) REVERT: x 304 TYR cc_start: 0.7910 (p90) cc_final: 0.7652 (p90) REVERT: x 326 MET cc_start: 0.8440 (mtp) cc_final: 0.8007 (mtp) REVERT: x 346 ASP cc_start: 0.8623 (t0) cc_final: 0.8416 (t0) REVERT: x 373 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7611 (mptt) REVERT: x 381 MET cc_start: 0.8491 (tpp) cc_final: 0.8014 (tpp) REVERT: x 488 GLN cc_start: 0.8500 (mt0) cc_final: 0.7919 (pp30) REVERT: x 577 MET cc_start: 0.8021 (mmm) cc_final: 0.7771 (mmm) REVERT: x 720 SER cc_start: 0.8935 (t) cc_final: 0.8643 (p) REVERT: x 721 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8736 (ttt90) REVERT: x 758 ASP cc_start: 0.8084 (m-30) cc_final: 0.7626 (m-30) REVERT: x 762 MET cc_start: 0.7482 (mmp) cc_final: 0.7257 (mmp) REVERT: x 796 GLN cc_start: 0.8251 (mt0) cc_final: 0.7533 (pt0) REVERT: x 851 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7758 (mttm) REVERT: y 109 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8234 (tm) outliers start: 23 outliers final: 14 residues processed: 115 average time/residue: 0.0745 time to fit residues: 11.4651 Evaluate side-chains 109 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 319 LEU Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 721 ARG Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 836 MET Chi-restraints excluded: chain x residue 837 LEU Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 96 GLU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN x 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.167374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119788 restraints weight = 7430.035| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.93 r_work: 0.3336 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6046 Z= 0.106 Angle : 0.632 9.534 8195 Z= 0.289 Chirality : 0.052 0.429 961 Planarity : 0.004 0.033 1008 Dihedral : 8.951 156.991 876 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 2.47 % Allowed : 13.87 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.32), residues: 714 helix: 0.20 (0.30), residues: 307 sheet: -0.09 (0.55), residues: 98 loop : -0.85 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG x 289 TYR 0.020 0.001 TYR x 304 PHE 0.014 0.001 PHE x 565 TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6046) covalent geometry : angle 0.63242 / 0.29 ( 8195) hydrogen bonds : bond 0.02961 / 1.89 ( 190) hydrogen bonds : angle 3.97435 / 2.84 ( 558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.151 Fit side-chains REVERT: x 245 MET cc_start: 0.7792 (ttm) cc_final: 0.7216 (mmt) REVERT: x 265 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7434 (t80) REVERT: x 304 TYR cc_start: 0.7731 (p90) cc_final: 0.7203 (p90) REVERT: x 326 MET cc_start: 0.8308 (mtp) cc_final: 0.7831 (mtp) REVERT: x 339 LYS cc_start: 0.8724 (mttt) cc_final: 0.8458 (mtpt) REVERT: x 346 ASP cc_start: 0.8604 (t0) cc_final: 0.8260 (t0) REVERT: x 347 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8446 (mm-30) REVERT: x 373 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7675 (mptt) REVERT: x 380 THR cc_start: 0.8993 (p) cc_final: 0.8576 (p) REVERT: x 381 MET cc_start: 0.8349 (tpp) cc_final: 0.7817 (tpp) REVERT: x 528 VAL cc_start: 0.8026 (t) cc_final: 0.7824 (m) REVERT: x 720 SER cc_start: 0.8930 (t) cc_final: 0.8616 (p) REVERT: x 758 ASP cc_start: 0.8072 (m-30) cc_final: 0.7598 (m-30) REVERT: x 796 GLN cc_start: 0.8214 (mt0) cc_final: 0.7438 (pt0) REVERT: x 851 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8020 (mmmm) REVERT: y 90 GLU cc_start: 0.7633 (tp30) cc_final: 0.7241 (tp30) REVERT: y 109 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8179 (tm) outliers start: 16 outliers final: 5 residues processed: 117 average time/residue: 0.0642 time to fit residues: 10.3593 Evaluate side-chains 103 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 256 LEU Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115659 restraints weight = 7439.628| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.96 r_work: 0.3303 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6046 Z= 0.172 Angle : 0.662 8.936 8195 Z= 0.310 Chirality : 0.053 0.393 961 Planarity : 0.004 0.031 1008 Dihedral : 8.884 153.658 874 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 2.77 % Allowed : 14.79 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.32), residues: 714 helix: 0.27 (0.30), residues: 308 sheet: -0.00 (0.55), residues: 96 loop : -0.90 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG x 289 TYR 0.018 0.002 TYR x 304 PHE 0.008 0.001 PHE x 863 TRP 0.009 0.001 TRP x 568 HIS 0.002 0.001 HIS y 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 6046) covalent geometry : angle 0.66202 / 0.31 ( 8195) hydrogen bonds : bond 0.03693 / 2.34 ( 190) hydrogen bonds : angle 4.16296 / 2.96 ( 558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7749 (ttm) cc_final: 0.7136 (mmt) REVERT: x 265 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7430 (t80) REVERT: x 289 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.7180 (mtm-85) REVERT: x 304 TYR cc_start: 0.7819 (p90) cc_final: 0.7537 (p90) REVERT: x 309 GLU cc_start: 0.7169 (mp0) cc_final: 0.6288 (tp30) REVERT: x 326 MET cc_start: 0.8374 (mtp) cc_final: 0.7855 (mtp) REVERT: x 339 LYS cc_start: 0.8731 (mttt) cc_final: 0.8456 (mtpt) REVERT: x 373 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7654 (mptt) REVERT: x 380 THR cc_start: 0.9014 (p) cc_final: 0.8577 (p) REVERT: x 381 MET cc_start: 0.8497 (tpp) cc_final: 0.7964 (tpp) REVERT: x 577 MET cc_start: 0.8319 (mmm) cc_final: 0.7992 (mmm) REVERT: x 720 SER cc_start: 0.8991 (t) cc_final: 0.8656 (p) REVERT: x 758 ASP cc_start: 0.8070 (m-30) cc_final: 0.7593 (m-30) REVERT: x 796 GLN cc_start: 0.8267 (mt0) cc_final: 0.7551 (pt0) REVERT: x 851 LYS cc_start: 0.8313 (mmtm) cc_final: 0.8033 (mmmm) REVERT: y 90 GLU cc_start: 0.7556 (tp30) cc_final: 0.7153 (tp30) REVERT: y 109 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8203 (tm) outliers start: 18 outliers final: 13 residues processed: 107 average time/residue: 0.0653 time to fit residues: 9.6185 Evaluate side-chains 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 256 LEU Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 319 LEU Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116378 restraints weight = 7449.268| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.96 r_work: 0.3280 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6046 Z= 0.146 Angle : 0.637 8.624 8195 Z= 0.299 Chirality : 0.051 0.396 961 Planarity : 0.004 0.030 1008 Dihedral : 8.745 151.722 874 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 3.08 % Allowed : 14.02 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.32), residues: 714 helix: 0.41 (0.30), residues: 307 sheet: -0.06 (0.55), residues: 96 loop : -0.83 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 289 TYR 0.017 0.001 TYR x 304 PHE 0.012 0.001 PHE x 565 TRP 0.009 0.001 TRP x 568 HIS 0.002 0.001 HIS y 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6046) covalent geometry : angle 0.63745 / 0.30 ( 8195) hydrogen bonds : bond 0.03398 / 2.15 ( 190) hydrogen bonds : angle 4.07906 / 2.91 ( 558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7801 (ttm) cc_final: 0.7347 (mmt) REVERT: x 265 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7447 (t80) REVERT: x 289 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7320 (mtm-85) REVERT: x 304 TYR cc_start: 0.7821 (p90) cc_final: 0.7486 (p90) REVERT: x 309 GLU cc_start: 0.7133 (mp0) cc_final: 0.6330 (tp30) REVERT: x 326 MET cc_start: 0.8386 (mtp) cc_final: 0.7811 (mtp) REVERT: x 339 LYS cc_start: 0.8701 (mttt) cc_final: 0.8440 (mtpt) REVERT: x 346 ASP cc_start: 0.8581 (t0) cc_final: 0.8252 (t0) REVERT: x 373 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7770 (mptt) REVERT: x 380 THR cc_start: 0.9022 (p) cc_final: 0.8610 (p) REVERT: x 381 MET cc_start: 0.8508 (tpp) cc_final: 0.8026 (tpp) REVERT: x 577 MET cc_start: 0.8200 (mmm) cc_final: 0.7846 (mmm) REVERT: x 720 SER cc_start: 0.8994 (t) cc_final: 0.8679 (p) REVERT: x 758 ASP cc_start: 0.8066 (m-30) cc_final: 0.7580 (m-30) REVERT: x 796 GLN cc_start: 0.8289 (mt0) cc_final: 0.7562 (pt0) REVERT: x 838 THR cc_start: 0.8805 (m) cc_final: 0.8602 (p) REVERT: x 851 LYS cc_start: 0.8300 (mmtm) cc_final: 0.8025 (mmmm) REVERT: y 90 GLU cc_start: 0.7542 (tp30) cc_final: 0.7123 (tp30) REVERT: y 109 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8236 (tm) outliers start: 20 outliers final: 13 residues processed: 109 average time/residue: 0.0606 time to fit residues: 9.0794 Evaluate side-chains 104 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 319 LEU Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114687 restraints weight = 7564.756| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.83 r_work: 0.3299 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6046 Z= 0.126 Angle : 0.624 8.915 8195 Z= 0.293 Chirality : 0.051 0.394 961 Planarity : 0.004 0.031 1008 Dihedral : 8.657 150.351 874 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 2.93 % Allowed : 14.33 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.32), residues: 714 helix: 0.51 (0.30), residues: 308 sheet: -0.13 (0.54), residues: 99 loop : -0.77 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 721 TYR 0.017 0.001 TYR x 304 PHE 0.031 0.001 PHE x 396 TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6046) covalent geometry : angle 0.62414 / 0.29 ( 8195) hydrogen bonds : bond 0.03202 / 2.04 ( 190) hydrogen bonds : angle 4.01132 / 2.86 ( 558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7682 (ttm) cc_final: 0.7458 (mmt) REVERT: x 265 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7428 (t80) REVERT: x 304 TYR cc_start: 0.7811 (p90) cc_final: 0.7490 (p90) REVERT: x 326 MET cc_start: 0.8371 (mtp) cc_final: 0.7768 (mtp) REVERT: x 346 ASP cc_start: 0.8490 (t0) cc_final: 0.8255 (t0) REVERT: x 373 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7870 (mptt) REVERT: x 380 THR cc_start: 0.9014 (p) cc_final: 0.8613 (p) REVERT: x 381 MET cc_start: 0.8520 (tpp) cc_final: 0.8146 (tpp) REVERT: x 397 ASN cc_start: 0.8916 (t0) cc_final: 0.8673 (t0) REVERT: x 528 VAL cc_start: 0.8083 (t) cc_final: 0.7871 (m) REVERT: x 577 MET cc_start: 0.8207 (mmm) cc_final: 0.7887 (mmm) REVERT: x 720 SER cc_start: 0.9011 (t) cc_final: 0.8721 (p) REVERT: x 758 ASP cc_start: 0.8027 (m-30) cc_final: 0.7565 (m-30) REVERT: x 796 GLN cc_start: 0.8322 (mt0) cc_final: 0.7623 (pt0) REVERT: x 851 LYS cc_start: 0.8234 (mmtm) cc_final: 0.8027 (mmmm) REVERT: x 858 MET cc_start: 0.8993 (mmm) cc_final: 0.8514 (tpt) REVERT: y 90 GLU cc_start: 0.7492 (tp30) cc_final: 0.7152 (tp30) REVERT: y 109 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8258 (tm) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.0641 time to fit residues: 10.0002 Evaluate side-chains 104 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 368 GLN Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111223 restraints weight = 7860.635| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.94 r_work: 0.3269 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6046 Z= 0.162 Angle : 0.654 8.108 8195 Z= 0.310 Chirality : 0.051 0.389 961 Planarity : 0.004 0.030 1008 Dihedral : 8.655 150.186 874 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.76 % Favored : 95.10 % Rotamer: Outliers : 2.93 % Allowed : 15.10 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.32), residues: 714 helix: 0.51 (0.30), residues: 311 sheet: -0.44 (0.53), residues: 109 loop : -0.62 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 289 TYR 0.016 0.002 TYR x 304 PHE 0.044 0.002 PHE x 396 TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 6046) covalent geometry : angle 0.65424 / 0.31 ( 8195) hydrogen bonds : bond 0.03550 / 2.27 ( 190) hydrogen bonds : angle 4.09880 / 2.92 ( 558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: x 227 GLN cc_start: 0.8665 (mp10) cc_final: 0.8381 (pt0) REVERT: x 245 MET cc_start: 0.7565 (ttm) cc_final: 0.7352 (mmt) REVERT: x 255 GLN cc_start: 0.8426 (mp10) cc_final: 0.8162 (mp10) REVERT: x 265 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7481 (t80) REVERT: x 304 TYR cc_start: 0.7903 (p90) cc_final: 0.7585 (p90) REVERT: x 309 GLU cc_start: 0.7283 (mp0) cc_final: 0.6351 (tp30) REVERT: x 326 MET cc_start: 0.8427 (mtp) cc_final: 0.7858 (mtp) REVERT: x 346 ASP cc_start: 0.8560 (t0) cc_final: 0.8305 (t0) REVERT: x 373 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7912 (mptt) REVERT: x 380 THR cc_start: 0.9021 (p) cc_final: 0.8654 (p) REVERT: x 381 MET cc_start: 0.8568 (tpp) cc_final: 0.8196 (tpp) REVERT: x 577 MET cc_start: 0.8290 (mmm) cc_final: 0.7974 (mmm) REVERT: x 720 SER cc_start: 0.9059 (t) cc_final: 0.8769 (p) REVERT: x 758 ASP cc_start: 0.8030 (m-30) cc_final: 0.7595 (m-30) REVERT: x 796 GLN cc_start: 0.8365 (mt0) cc_final: 0.7688 (pt0) REVERT: x 858 MET cc_start: 0.8996 (mmm) cc_final: 0.8516 (tpt) REVERT: y 90 GLU cc_start: 0.7539 (tp30) cc_final: 0.7190 (tp30) REVERT: y 109 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8306 (tm) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.0605 time to fit residues: 8.7022 Evaluate side-chains 100 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 319 LEU Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115814 restraints weight = 7560.634| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.82 r_work: 0.3320 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6046 Z= 0.113 Angle : 0.618 9.158 8195 Z= 0.293 Chirality : 0.050 0.412 961 Planarity : 0.004 0.030 1008 Dihedral : 8.553 149.697 874 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 2.16 % Allowed : 15.56 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.32), residues: 714 helix: 0.74 (0.30), residues: 309 sheet: -0.40 (0.53), residues: 111 loop : -0.58 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 495 TYR 0.017 0.001 TYR x 304 PHE 0.033 0.001 PHE x 396 TRP 0.007 0.001 TRP x 568 HIS 0.002 0.001 HIS x 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 6046) covalent geometry : angle 0.61839 / 0.29 ( 8195) hydrogen bonds : bond 0.02917 / 1.88 ( 190) hydrogen bonds : angle 3.88527 / 2.77 ( 558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: x 227 GLN cc_start: 0.8683 (mp10) cc_final: 0.8443 (pt0) REVERT: x 245 MET cc_start: 0.7786 (ttm) cc_final: 0.7375 (mmt) REVERT: x 255 GLN cc_start: 0.8360 (mp10) cc_final: 0.8075 (mp10) REVERT: x 265 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7472 (t80) REVERT: x 304 TYR cc_start: 0.7753 (p90) cc_final: 0.7148 (p90) REVERT: x 326 MET cc_start: 0.8347 (mtp) cc_final: 0.7756 (mtp) REVERT: x 346 ASP cc_start: 0.8500 (t0) cc_final: 0.8230 (t0) REVERT: x 380 THR cc_start: 0.9014 (p) cc_final: 0.8654 (p) REVERT: x 381 MET cc_start: 0.8543 (tpp) cc_final: 0.8166 (tpp) REVERT: x 577 MET cc_start: 0.8241 (mmm) cc_final: 0.7914 (mmm) REVERT: x 720 SER cc_start: 0.9010 (t) cc_final: 0.8736 (p) REVERT: x 796 GLN cc_start: 0.8282 (mt0) cc_final: 0.7572 (pt0) REVERT: x 858 MET cc_start: 0.8966 (mmm) cc_final: 0.8506 (tpt) REVERT: y 90 GLU cc_start: 0.7494 (tp30) cc_final: 0.7151 (tp30) REVERT: y 109 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8272 (tm) outliers start: 14 outliers final: 9 residues processed: 111 average time/residue: 0.0650 time to fit residues: 10.0444 Evaluate side-chains 102 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.164966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118949 restraints weight = 7477.858| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.80 r_work: 0.3358 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 6046 Z= 0.105 Angle : 0.617 9.274 8195 Z= 0.293 Chirality : 0.049 0.418 961 Planarity : 0.004 0.030 1008 Dihedral : 8.463 148.558 874 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 1.85 % Allowed : 16.80 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.32), residues: 714 helix: 0.83 (0.30), residues: 306 sheet: -0.39 (0.52), residues: 115 loop : -0.52 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 495 TYR 0.017 0.001 TYR x 304 PHE 0.030 0.001 PHE x 396 TRP 0.006 0.001 TRP x 568 HIS 0.002 0.000 HIS x 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6046) covalent geometry : angle 0.61741 / 0.29 ( 8195) hydrogen bonds : bond 0.02726 / 1.77 ( 190) hydrogen bonds : angle 3.78916 / 2.69 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.98 seconds wall clock time: 30 minutes 43.62 seconds (1843.62 seconds total)