Starting phenix.real_space_refine on Sun Mar 10 23:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/03_2024/7dd3_30643.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/03_2024/7dd3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/03_2024/7dd3_30643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/03_2024/7dd3_30643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/03_2024/7dd3_30643.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/03_2024/7dd3_30643.pdb" } resolution = 3.2 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= 0.000 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 Residue "x ARG 401": "NH1" <-> "NH2" Residue "x ARG 402": "NH1" <-> "NH2" Residue "x ARG 465": "NH1" <-> "NH2" Residue "y GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'RNA': 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: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 3.89, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 2.38 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: 2.14 Time building geometry restraints manager: 2.37 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: 96.36 - 103.90: 121 103.90 - 111.43: 2624 111.43 - 118.96: 2335 118.96 - 126.50: 3041 126.50 - 134.03: 74 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: 3492 16.59 - 33.19: 166 33.19 - 49.78: 62 49.78 - 66.37: 21 66.37 - 82.96: 3 Dihedral angle restraints: 3744 sinusoidal: 1635 harmonic: 2109 Sorted by residual: dihedral pdb=" C THR y 93 " pdb=" N THR y 93 " pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta harmonic sigma weight residual -122.00 -134.68 12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" N THR y 93 " pdb=" C THR y 93 " pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta harmonic sigma weight residual 123.40 135.17 -11.77 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA ARG x 584 " pdb=" C ARG x 584 " pdb=" N THR x 585 " pdb=" CA THR x 585 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 742 0.074 - 0.148: 200 0.148 - 0.222: 16 0.222 - 0.296: 1 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=" CA THR x 681 " pdb=" N THR x 681 " pdb=" C THR x 681 " pdb=" CB THR x 681 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+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 2.520 nonbonded pdb=" O LEU x 337 " pdb=" NH1 ARG x 369 " model vdw 2.362 2.520 nonbonded pdb=" O LEU x 508 " pdb=" NH2 ARG x 552 " model vdw 2.363 2.520 nonbonded pdb=" O ALA x 420 " pdb=" OG1 THR x 424 " model vdw 2.399 2.440 nonbonded pdb=" NZ LYS x 363 " pdb=" O PHE x 389 " model vdw 2.411 2.520 ... (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 ========== 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: 0.590 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: 2.010 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.520 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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= 0.769 Angle : 1.056 10.087 8195 Z= 0.562 Chirality : 0.064 0.370 961 Planarity : 0.008 0.055 1008 Dihedral : 12.444 82.961 2376 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 (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: -3.77 (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 TRP 0.026 0.004 TRP x 568 HIS 0.009 0.002 HIS y 142 PHE 0.039 0.004 PHE x 783 TYR 0.033 0.004 TYR x 795 ARG 0.013 0.002 ARG x 844 *********************** 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 fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 0.690 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: 0.8134 (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: 0.2186 time to fit residues: 47.1200 Evaluate side-chains 100 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 40.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 239 ASN x 382 ASN x 412 GLN x 419 HIS x 427 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6046 Z= 0.236 Angle : 0.638 9.600 8195 Z= 0.332 Chirality : 0.045 0.238 961 Planarity : 0.005 0.041 1008 Dihedral : 10.966 69.444 919 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.36 % Favored : 96.50 % Rotamer: Outliers : 4.01 % Allowed : 8.32 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.22 (0.29), residues: 714 helix: -1.63 (0.25), residues: 306 sheet: -0.42 (0.53), residues: 96 loop : -1.51 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP x 568 HIS 0.007 0.001 HIS x 429 PHE 0.013 0.002 PHE x 863 TYR 0.028 0.002 TYR x 304 ARG 0.004 0.000 ARG x 289 *********************** 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 134 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 256 LEU cc_start: 0.8984 (mm) cc_final: 0.8578 (mm) REVERT: x 265 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7240 (t80) REVERT: x 488 GLN cc_start: 0.8103 (mt0) cc_final: 0.7695 (pp30) REVERT: x 796 GLN cc_start: 0.7986 (mt0) cc_final: 0.7709 (pt0) REVERT: y 90 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: y 109 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8439 (tm) outliers start: 26 outliers final: 11 residues processed: 126 average time/residue: 0.1798 time to fit residues: 29.8882 Evaluate side-chains 100 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 534 THR 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 93 THR 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 36 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 258 GLN x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2954 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= 0.261 Angle : 0.600 9.563 8195 Z= 0.305 Chirality : 0.045 0.209 961 Planarity : 0.005 0.039 1008 Dihedral : 10.185 60.203 911 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.70 % Allowed : 11.09 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.31 (0.31), residues: 714 helix: -0.67 (0.28), residues: 308 sheet: -0.07 (0.56), residues: 96 loop : -1.22 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 568 HIS 0.003 0.001 HIS x 572 PHE 0.016 0.002 PHE x 562 TYR 0.032 0.002 TYR x 304 ARG 0.005 0.000 ARG x 289 *********************** 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 119 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.729 Fit side-chains REVERT: x 245 MET cc_start: 0.7168 (ttm) cc_final: 0.6610 (mmt) REVERT: x 265 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7236 (t80) REVERT: x 373 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7852 (mptt) REVERT: x 488 GLN cc_start: 0.8129 (mt0) cc_final: 0.7781 (pp30) REVERT: x 796 GLN cc_start: 0.7994 (mt0) cc_final: 0.7728 (pt0) REVERT: y 109 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8432 (tm) outliers start: 24 outliers final: 11 residues processed: 111 average time/residue: 0.1755 time to fit residues: 26.0433 Evaluate side-chains 96 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 808 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 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 50.0000 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6046 Z= 0.158 Angle : 0.536 8.261 8195 Z= 0.272 Chirality : 0.043 0.155 961 Planarity : 0.004 0.034 1008 Dihedral : 9.824 61.135 908 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 3.08 % Allowed : 11.86 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.84 (0.32), residues: 714 helix: -0.12 (0.29), residues: 311 sheet: 0.03 (0.56), residues: 96 loop : -1.11 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP x 714 HIS 0.001 0.000 HIS y 142 PHE 0.020 0.001 PHE x 565 TYR 0.012 0.001 TYR x 515 ARG 0.006 0.000 ARG x 289 *********************** 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 119 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.648 Fit side-chains REVERT: x 265 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7299 (t80) REVERT: x 304 TYR cc_start: 0.8037 (p90) cc_final: 0.7830 (p90) REVERT: x 373 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7794 (mptt) REVERT: x 380 THR cc_start: 0.8518 (p) cc_final: 0.8257 (p) REVERT: x 488 GLN cc_start: 0.8097 (mt0) cc_final: 0.7895 (pp30) REVERT: x 725 GLN cc_start: 0.8405 (mt0) cc_final: 0.8142 (mp10) REVERT: x 796 GLN cc_start: 0.7938 (mt0) cc_final: 0.7709 (pt0) REVERT: y 109 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (tm) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 0.1866 time to fit residues: 27.6477 Evaluate side-chains 96 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 338 SER Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 481 GLU Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 808 SER Chi-restraints excluded: chain x residue 837 LEU 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 57 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6046 Z= 0.198 Angle : 0.522 7.346 8195 Z= 0.267 Chirality : 0.043 0.178 961 Planarity : 0.004 0.033 1008 Dihedral : 9.739 61.551 908 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 3.39 % Allowed : 13.87 % 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 (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: -0.56 (0.32), residues: 714 helix: 0.18 (0.30), residues: 308 sheet: 0.03 (0.55), residues: 96 loop : -0.97 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 714 HIS 0.002 0.001 HIS y 142 PHE 0.016 0.001 PHE x 565 TYR 0.011 0.002 TYR x 475 ARG 0.006 0.000 ARG x 289 *********************** 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 113 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.698 Fit side-chains REVERT: x 255 GLN cc_start: 0.7938 (mp10) cc_final: 0.7330 (mp10) REVERT: x 265 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7281 (t80) REVERT: x 304 TYR cc_start: 0.8045 (p90) cc_final: 0.7771 (p90) REVERT: x 326 MET cc_start: 0.8097 (mtp) cc_final: 0.7856 (mtp) REVERT: x 347 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7868 (mm-30) REVERT: x 373 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7806 (mptt) REVERT: x 381 MET cc_start: 0.7972 (tpp) cc_final: 0.7517 (tpp) REVERT: x 796 GLN cc_start: 0.7965 (mt0) cc_final: 0.7709 (pt0) REVERT: y 109 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8496 (tm) outliers start: 22 outliers final: 13 residues processed: 108 average time/residue: 0.1745 time to fit residues: 25.2779 Evaluate side-chains 97 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 481 GLU Chi-restraints excluded: chain x residue 502 ASN 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 720 SER Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 808 SER Chi-restraints excluded: chain y residue 71 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 23 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 67 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6046 Z= 0.142 Angle : 0.511 6.865 8195 Z= 0.259 Chirality : 0.042 0.168 961 Planarity : 0.004 0.032 1008 Dihedral : 9.603 64.131 906 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 2.47 % Allowed : 15.10 % 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 (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: -0.32 (0.32), residues: 714 helix: 0.48 (0.30), residues: 307 sheet: -0.10 (0.55), residues: 98 loop : -0.87 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 PHE 0.012 0.001 PHE x 565 TYR 0.011 0.001 TYR x 321 ARG 0.005 0.000 ARG x 289 *********************** 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 108 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.716 Fit side-chains REVERT: x 255 GLN cc_start: 0.7961 (mp10) cc_final: 0.7372 (mp10) REVERT: x 265 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7281 (t80) REVERT: x 289 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7351 (mtm-85) REVERT: x 304 TYR cc_start: 0.8002 (p90) cc_final: 0.7778 (p90) REVERT: x 326 MET cc_start: 0.8053 (mtp) cc_final: 0.7835 (mtp) REVERT: x 796 GLN cc_start: 0.7925 (mt0) cc_final: 0.7678 (pt0) REVERT: y 109 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8448 (tm) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 0.1703 time to fit residues: 23.9999 Evaluate side-chains 95 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 339 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 481 GLU Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 513 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6046 Z= 0.151 Angle : 0.515 6.762 8195 Z= 0.261 Chirality : 0.042 0.174 961 Planarity : 0.004 0.032 1008 Dihedral : 9.523 65.256 906 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 2.93 % Allowed : 15.41 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.32), residues: 714 helix: 0.60 (0.30), residues: 308 sheet: -0.25 (0.54), residues: 108 loop : -0.66 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 429 PHE 0.009 0.001 PHE x 562 TYR 0.010 0.001 TYR x 403 ARG 0.004 0.000 ARG x 721 *********************** 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 105 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.725 Fit side-chains REVERT: x 245 MET cc_start: 0.7081 (mmt) cc_final: 0.6680 (mmt) REVERT: x 255 GLN cc_start: 0.7993 (mp10) cc_final: 0.7373 (mp10) REVERT: x 265 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7336 (t80) REVERT: x 304 TYR cc_start: 0.7942 (p90) cc_final: 0.7698 (p90) REVERT: x 373 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7920 (mptt) REVERT: x 796 GLN cc_start: 0.7930 (mt0) cc_final: 0.7689 (pt0) REVERT: y 109 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8466 (tm) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.1834 time to fit residues: 24.6894 Evaluate side-chains 96 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 339 LYS 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 481 GLU Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 513 ILE 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 720 SER Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 808 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 92 VAL 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 20 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7808 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6046 Z= 0.137 Angle : 0.509 6.763 8195 Z= 0.258 Chirality : 0.042 0.168 961 Planarity : 0.004 0.032 1008 Dihedral : 9.480 66.038 906 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 2.93 % Allowed : 15.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.32), residues: 714 helix: 0.65 (0.31), residues: 313 sheet: -0.25 (0.54), residues: 111 loop : -0.54 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 714 HIS 0.002 0.001 HIS x 429 PHE 0.011 0.001 PHE x 565 TYR 0.011 0.001 TYR x 259 ARG 0.004 0.000 ARG x 721 *********************** 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 106 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.690 Fit side-chains REVERT: x 245 MET cc_start: 0.7386 (mmt) cc_final: 0.6983 (mmt) REVERT: x 255 GLN cc_start: 0.8023 (mp10) cc_final: 0.7407 (mp10) REVERT: x 265 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7327 (t80) REVERT: x 304 TYR cc_start: 0.7872 (p90) cc_final: 0.7598 (p90) REVERT: x 373 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7937 (mptt) REVERT: x 796 GLN cc_start: 0.7893 (mt0) cc_final: 0.7653 (pt0) REVERT: y 109 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8438 (tm) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.1649 time to fit residues: 22.9654 Evaluate side-chains 99 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 502 ASN 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 720 SER Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 808 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 92 VAL 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 66 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6046 Z= 0.131 Angle : 0.502 7.296 8195 Z= 0.253 Chirality : 0.041 0.167 961 Planarity : 0.004 0.034 1008 Dihedral : 9.435 66.911 906 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 2.62 % Allowed : 16.49 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.33), residues: 714 helix: 0.72 (0.31), residues: 313 sheet: 0.13 (0.56), residues: 101 loop : -0.67 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 568 HIS 0.002 0.000 HIS x 226 PHE 0.009 0.001 PHE x 562 TYR 0.010 0.001 TYR x 403 ARG 0.004 0.000 ARG x 289 *********************** 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 108 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.649 Fit side-chains REVERT: x 245 MET cc_start: 0.7426 (mmt) cc_final: 0.7012 (mmt) REVERT: x 255 GLN cc_start: 0.7941 (mp10) cc_final: 0.7355 (mp10) REVERT: x 265 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6764 (t80) REVERT: x 304 TYR cc_start: 0.7810 (p90) cc_final: 0.7554 (p90) REVERT: x 373 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7934 (mppt) REVERT: x 796 GLN cc_start: 0.7912 (mt0) cc_final: 0.7648 (pt0) REVERT: y 109 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8399 (tm) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 0.1767 time to fit residues: 24.7982 Evaluate side-chains 101 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE 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 502 ASN 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 720 SER Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 92 VAL 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 32 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 44 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 429 HIS x 725 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6046 Z= 0.178 Angle : 0.534 8.808 8195 Z= 0.269 Chirality : 0.042 0.161 961 Planarity : 0.004 0.033 1008 Dihedral : 9.418 65.459 906 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % Rotamer: Outliers : 3.08 % Allowed : 15.72 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.08 (0.33), residues: 714 helix: 0.73 (0.31), residues: 313 sheet: 0.08 (0.56), residues: 101 loop : -0.58 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 PHE 0.013 0.001 PHE x 565 TYR 0.011 0.001 TYR x 403 ARG 0.003 0.000 ARG x 289 ********************** 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 fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.726 Fit side-chains REVERT: x 245 MET cc_start: 0.7486 (mmt) cc_final: 0.7080 (mmt) REVERT: x 255 GLN cc_start: 0.7993 (mp10) cc_final: 0.7334 (mp10) REVERT: x 265 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6787 (t80) REVERT: x 373 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7992 (mppt) REVERT: x 721 ARG cc_start: 0.8655 (tpt-90) cc_final: 0.8150 (tpt-90) REVERT: x 725 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8033 (mp10) REVERT: x 796 GLN cc_start: 0.7936 (mt0) cc_final: 0.7689 (pt0) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.1712 time to fit residues: 25.0465 Evaluate side-chains 104 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE 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 502 ASN 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 720 SER Chi-restraints excluded: chain x residue 725 GLN Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 808 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 92 VAL 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 52 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.162611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115576 restraints weight = 7636.022| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.89 r_work: 0.3321 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 6046 Z= 0.277 Angle : 1.005 59.189 8195 Z= 0.607 Chirality : 0.044 0.373 961 Planarity : 0.004 0.042 1008 Dihedral : 9.422 65.459 906 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % Rotamer: Outliers : 2.31 % Allowed : 17.10 % Favored : 80.59 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.33), residues: 714 helix: 0.67 (0.31), residues: 313 sheet: 0.09 (0.56), residues: 101 loop : -0.58 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 714 HIS 0.001 0.001 HIS x 727 PHE 0.007 0.001 PHE x 863 TYR 0.010 0.001 TYR x 475 ARG 0.003 0.000 ARG x 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.32 seconds wall clock time: 32 minutes 14.58 seconds (1934.58 seconds total)