Starting phenix.real_space_refine on Thu Feb 15 20:52:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/02_2024/6vef_21156_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/02_2024/6vef_21156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/02_2024/6vef_21156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/02_2024/6vef_21156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/02_2024/6vef_21156_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/02_2024/6vef_21156_updated.pdb" } resolution = 4.08 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 2 5.49 5 S 66 5.16 5 C 8434 2.51 5 N 2400 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 612": "NH1" <-> "NH2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 900": "NH1" <-> "NH2" Residue "A ARG 904": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ARG 612": "NH1" <-> "NH2" Residue "B ARG 763": "NH1" <-> "NH2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 783": "NH1" <-> "NH2" Residue "B ARG 900": "NH1" <-> "NH2" Residue "B ARG 904": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6675 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 39, 'TRANS': 804} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6675 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 39, 'TRANS': 804} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'OAA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'OAA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Time building chain proxies: 7.24, per 1000 atoms: 0.54 Number of scatterers: 13414 At special positions: 0 Unit cell: (116.641, 106.117, 127.165, 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 66 16.00 P 2 15.00 O 2512 8.00 N 2400 7.00 C 8434 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: 5.09 Conformation dependent library (CDL) restraints added in 2.3 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 10 sheets defined 34.6% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 86 through 101 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 365 through 374 removed outlier: 4.658A pdb=" N LYS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 532 through 535 Proline residue: A 535 - end of helix No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 593 through 607 removed outlier: 3.536A pdb=" N ASP A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 672 Processing helix chain 'A' and resid 688 through 691 Processing helix chain 'A' and resid 695 through 699 Processing helix chain 'A' and resid 704 through 707 No H-bonds generated for 'chain 'A' and resid 704 through 707' Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 754 through 765 Processing helix chain 'A' and resid 780 through 783 removed outlier: 3.605A pdb=" N ARG A 783 " --> pdb=" O SER A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 783' Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 823 through 832 Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 885 through 892 removed outlier: 5.009A pdb=" N ARG A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 929 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 197 through 220 Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 365 through 374 removed outlier: 4.658A pdb=" N LYS B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 532 through 535 Proline residue: B 535 - end of helix No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 593 through 607 removed outlier: 3.536A pdb=" N ASP B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 607 " --> pdb=" O THR B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 672 Processing helix chain 'B' and resid 688 through 691 Processing helix chain 'B' and resid 695 through 699 Processing helix chain 'B' and resid 704 through 707 No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 735 through 737 No H-bonds generated for 'chain 'B' and resid 735 through 737' Processing helix chain 'B' and resid 754 through 765 Processing helix chain 'B' and resid 780 through 783 removed outlier: 3.605A pdb=" N ARG B 783 " --> pdb=" O SER B 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 780 through 783' Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 823 through 832 Processing helix chain 'B' and resid 853 through 858 Processing helix chain 'B' and resid 885 through 892 removed outlier: 5.009A pdb=" N ARG B 890 " --> pdb=" O GLN B 886 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 929 Processing sheet with id= A, first strand: chain 'A' and resid 168 through 171 Processing sheet with id= B, first strand: chain 'A' and resid 253 through 258 removed outlier: 6.891A pdb=" N VAL A 384 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N HIS A 355 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 386 " --> pdb=" O HIS A 355 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL A 448 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL A 387 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 450 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN A 389 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 452 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 301 through 306 Processing sheet with id= D, first strand: chain 'A' and resid 611 through 613 removed outlier: 6.243A pdb=" N LEU A 679 " --> pdb=" O ARG A 612 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A 715 " --> pdb=" O TRP A 682 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU A 773 " --> pdb=" O MET A 716 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU A 718 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL A 775 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN A 747 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N MET A 776 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N CYS A 749 " --> pdb=" O MET A 776 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 840 through 844 removed outlier: 6.540A pdb=" N ARG A 816 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 843 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 818 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 817 " --> pdb=" O ASP A 868 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER A 898 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TRP A 871 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG A 900 " --> pdb=" O TRP A 871 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 168 through 171 Processing sheet with id= G, first strand: chain 'B' and resid 253 through 258 removed outlier: 6.892A pdb=" N VAL B 384 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N HIS B 355 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 386 " --> pdb=" O HIS B 355 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL B 448 " --> pdb=" O ARG B 385 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 387 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE B 450 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN B 389 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 452 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 301 through 306 Processing sheet with id= I, first strand: chain 'B' and resid 611 through 613 removed outlier: 6.242A pdb=" N LEU B 679 " --> pdb=" O ARG B 612 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 715 " --> pdb=" O TRP B 682 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 773 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 718 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 775 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLN B 747 " --> pdb=" O VAL B 774 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N MET B 776 " --> pdb=" O GLN B 747 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS B 749 " --> pdb=" O MET B 776 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 840 through 844 removed outlier: 6.541A pdb=" N ARG B 816 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL B 843 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL B 818 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B 817 " --> pdb=" O ASP B 868 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 898 " --> pdb=" O PHE B 869 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TRP B 871 " --> pdb=" O SER B 898 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG B 900 " --> pdb=" O TRP B 871 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4485 1.34 - 1.46: 2920 1.46 - 1.58: 6201 1.58 - 1.70: 2 1.70 - 1.82: 114 Bond restraints: 13722 Sorted by residual: bond pdb=" C3 OAA A1002 " pdb=" O3 OAA A1002 " ideal model delta sigma weight residual 1.214 1.305 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C3 OAA B1001 " pdb=" O3 OAA B1001 " ideal model delta sigma weight residual 1.214 1.304 -0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C4 OAA B1001 " pdb=" O4 OAA B1001 " ideal model delta sigma weight residual 1.241 1.305 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C4 OAA A1002 " pdb=" O4 OAA A1002 " ideal model delta sigma weight residual 1.241 1.305 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CA TRP B 871 " pdb=" CB TRP B 871 " ideal model delta sigma weight residual 1.527 1.451 0.076 2.48e-02 1.63e+03 9.47e+00 ... (remaining 13717 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.35: 323 105.35 - 113.21: 7355 113.21 - 121.06: 7031 121.06 - 128.91: 3732 128.91 - 136.76: 137 Bond angle restraints: 18578 Sorted by residual: angle pdb=" CA SER B 373 " pdb=" C SER B 373 " pdb=" N LYS B 374 " ideal model delta sigma weight residual 116.84 125.79 -8.95 1.71e+00 3.42e-01 2.74e+01 angle pdb=" CA SER A 373 " pdb=" C SER A 373 " pdb=" N LYS A 374 " ideal model delta sigma weight residual 116.84 125.78 -8.94 1.71e+00 3.42e-01 2.74e+01 angle pdb=" C GLY A 393 " pdb=" N PHE A 394 " pdb=" CA PHE A 394 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 angle pdb=" N GLY B 142 " pdb=" CA GLY B 142 " pdb=" C GLY B 142 " ideal model delta sigma weight residual 113.18 102.21 10.97 2.37e+00 1.78e-01 2.14e+01 angle pdb=" CA TYR A 883 " pdb=" CB TYR A 883 " pdb=" CG TYR A 883 " ideal model delta sigma weight residual 113.90 105.78 8.12 1.80e+00 3.09e-01 2.03e+01 ... (remaining 18573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.90: 8015 25.90 - 51.79: 193 51.79 - 77.69: 14 77.69 - 103.58: 0 103.58 - 129.48: 2 Dihedral angle restraints: 8224 sinusoidal: 3362 harmonic: 4862 Sorted by residual: dihedral pdb=" CA GLU A 728 " pdb=" C GLU A 728 " pdb=" N HIS A 729 " pdb=" CA HIS A 729 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU B 728 " pdb=" C GLU B 728 " pdb=" N HIS B 729 " pdb=" CA HIS B 729 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA TYR A 883 " pdb=" C TYR A 883 " pdb=" N CYS A 884 " pdb=" CA CYS A 884 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1527 0.075 - 0.150: 410 0.150 - 0.225: 48 0.225 - 0.300: 3 0.300 - 0.375: 2 Chirality restraints: 1990 Sorted by residual: chirality pdb=" CB ILE A 609 " pdb=" CA ILE A 609 " pdb=" CG1 ILE A 609 " pdb=" CG2 ILE A 609 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE B 609 " pdb=" CA ILE B 609 " pdb=" CG1 ILE B 609 " pdb=" CG2 ILE B 609 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ASN A 140 " pdb=" N ASN A 140 " pdb=" C ASN A 140 " pdb=" CB ASN A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1987 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 829 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LEU A 829 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 829 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 830 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 829 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C LEU B 829 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU B 829 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 830 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 398 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 399 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " 0.037 5.00e-02 4.00e+02 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 111 2.47 - 3.08: 8877 3.08 - 3.69: 21860 3.69 - 4.29: 30690 4.29 - 4.90: 49290 Nonbonded interactions: 110828 Sorted by model distance: nonbonded pdb=" OE1 GLU B 368 " pdb=" OG SER B 660 " model vdw 1.866 2.440 nonbonded pdb=" O LEU B 740 " pdb=" OH TYR B 849 " model vdw 2.197 2.440 nonbonded pdb=" O LEU A 740 " pdb=" OH TYR A 849 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR B 164 " pdb=" OE1 GLU B 189 " model vdw 2.256 2.440 nonbonded pdb=" OG SER B 909 " pdb=" O ALA B 911 " model vdw 2.264 2.440 ... (remaining 110823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 84 through 933) selection = (chain 'B' and resid 84 through 933) } 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 group one per residue 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: 0.380 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: 2.630 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 36.150 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.009 0.091 13722 Z= 0.605 Angle : 1.185 10.973 18578 Z= 0.639 Chirality : 0.066 0.375 1990 Planarity : 0.008 0.066 2454 Dihedral : 11.761 129.480 5100 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.39 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.48 (0.16), residues: 1684 helix: -2.88 (0.15), residues: 654 sheet: -2.70 (0.32), residues: 190 loop : -3.12 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 708 HIS 0.017 0.003 HIS B 460 PHE 0.041 0.004 PHE B 203 TYR 0.022 0.004 TYR A 849 ARG 0.010 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.654 Fit side-chains REVERT: A 173 MET cc_start: 0.7556 (tpp) cc_final: 0.6183 (tpp) REVERT: A 624 PHE cc_start: 0.7877 (t80) cc_final: 0.7635 (t80) REVERT: A 659 LEU cc_start: 0.8176 (tt) cc_final: 0.7969 (tp) REVERT: A 776 MET cc_start: 0.8625 (mmp) cc_final: 0.8178 (mmm) REVERT: B 101 PHE cc_start: 0.7334 (m-80) cc_final: 0.6576 (m-80) REVERT: B 173 MET cc_start: 0.7558 (tpp) cc_final: 0.6344 (tpp) REVERT: B 624 PHE cc_start: 0.7858 (t80) cc_final: 0.7647 (t80) REVERT: B 776 MET cc_start: 0.8601 (mmp) cc_final: 0.8153 (mmm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2374 time to fit residues: 87.3094 Evaluate side-chains 141 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 185 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS A 390 ASN A 631 HIS A 694 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 185 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 390 ASN B 631 HIS B 694 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13722 Z= 0.300 Angle : 0.736 8.226 18578 Z= 0.376 Chirality : 0.047 0.209 1990 Planarity : 0.006 0.054 2454 Dihedral : 7.972 119.248 1864 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.36 (0.18), residues: 1684 helix: -1.54 (0.18), residues: 658 sheet: -2.70 (0.30), residues: 216 loop : -2.66 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 871 HIS 0.005 0.001 HIS A 888 PHE 0.014 0.002 PHE B 700 TYR 0.017 0.002 TYR B 669 ARG 0.004 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.813 Fit side-chains REVERT: A 584 MET cc_start: 0.7365 (mtp) cc_final: 0.6931 (mtp) REVERT: B 101 PHE cc_start: 0.7315 (m-80) cc_final: 0.7059 (m-80) REVERT: B 584 MET cc_start: 0.7347 (mtp) cc_final: 0.6911 (mtp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2051 time to fit residues: 62.8970 Evaluate side-chains 145 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN A 764 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13722 Z= 0.437 Angle : 0.801 7.976 18578 Z= 0.406 Chirality : 0.049 0.171 1990 Planarity : 0.006 0.051 2454 Dihedral : 7.865 113.996 1864 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.07 (0.19), residues: 1684 helix: -1.19 (0.19), residues: 662 sheet: -2.69 (0.33), residues: 190 loop : -2.60 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 871 HIS 0.007 0.002 HIS B 322 PHE 0.028 0.003 PHE A 624 TYR 0.018 0.003 TYR B 509 ARG 0.006 0.001 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.496 Fit side-chains REVERT: A 211 GLU cc_start: 0.6752 (pp20) cc_final: 0.6491 (pp20) REVERT: B 101 PHE cc_start: 0.7392 (m-80) cc_final: 0.7075 (m-80) REVERT: B 173 MET cc_start: 0.7987 (tpp) cc_final: 0.6514 (tpp) REVERT: B 238 MET cc_start: 0.8213 (ttp) cc_final: 0.7977 (ttt) REVERT: B 716 MET cc_start: 0.8836 (mmm) cc_final: 0.8635 (mmm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2444 time to fit residues: 68.1740 Evaluate side-chains 134 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 HIS ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13722 Z= 0.209 Angle : 0.652 8.468 18578 Z= 0.327 Chirality : 0.045 0.137 1990 Planarity : 0.005 0.041 2454 Dihedral : 7.281 114.888 1864 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.19), residues: 1684 helix: -0.79 (0.20), residues: 658 sheet: -2.71 (0.31), residues: 202 loop : -2.43 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 871 HIS 0.003 0.001 HIS B 914 PHE 0.018 0.002 PHE B 624 TYR 0.018 0.002 TYR A 849 ARG 0.004 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.834 Fit side-chains REVERT: A 211 GLU cc_start: 0.6679 (pp20) cc_final: 0.6443 (pp20) REVERT: A 584 MET cc_start: 0.7335 (mtp) cc_final: 0.6835 (mtp) REVERT: A 722 TYR cc_start: 0.8570 (m-80) cc_final: 0.8349 (m-80) REVERT: A 875 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7430 (mt-10) REVERT: B 101 PHE cc_start: 0.7320 (m-80) cc_final: 0.6820 (m-80) REVERT: B 173 MET cc_start: 0.7912 (tpp) cc_final: 0.6434 (tpp) REVERT: B 584 MET cc_start: 0.7307 (mtp) cc_final: 0.6802 (mtp) REVERT: B 875 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7475 (mt-10) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2352 time to fit residues: 72.0347 Evaluate side-chains 141 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN B 248 ASN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13722 Z= 0.231 Angle : 0.649 7.575 18578 Z= 0.324 Chirality : 0.045 0.246 1990 Planarity : 0.004 0.038 2454 Dihedral : 7.066 115.162 1864 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.20), residues: 1684 helix: -0.60 (0.20), residues: 652 sheet: -2.55 (0.29), residues: 220 loop : -2.38 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 871 HIS 0.004 0.001 HIS A 322 PHE 0.019 0.002 PHE A 624 TYR 0.020 0.002 TYR A 849 ARG 0.004 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.651 Fit side-chains REVERT: A 189 GLU cc_start: 0.5586 (tt0) cc_final: 0.5193 (tt0) REVERT: A 408 MET cc_start: 0.4706 (mmp) cc_final: 0.4111 (mmp) REVERT: A 492 GLU cc_start: 0.8323 (tt0) cc_final: 0.8056 (tt0) REVERT: A 584 MET cc_start: 0.7441 (mtp) cc_final: 0.7104 (mtp) REVERT: A 598 ASN cc_start: 0.8318 (p0) cc_final: 0.7823 (t0) REVERT: A 875 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7690 (mt-10) REVERT: B 101 PHE cc_start: 0.7253 (m-80) cc_final: 0.6763 (m-80) REVERT: B 173 MET cc_start: 0.7917 (tpp) cc_final: 0.6429 (tpp) REVERT: B 189 GLU cc_start: 0.4084 (tm-30) cc_final: 0.3811 (tm-30) REVERT: B 492 GLU cc_start: 0.8340 (tt0) cc_final: 0.8063 (tt0) REVERT: B 581 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7400 (ttm170) REVERT: B 584 MET cc_start: 0.7395 (mtp) cc_final: 0.7057 (mtp) REVERT: B 598 ASN cc_start: 0.8385 (p0) cc_final: 0.7831 (t0) REVERT: B 875 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7600 (mt-10) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2176 time to fit residues: 71.3666 Evaluate side-chains 149 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13722 Z= 0.257 Angle : 0.671 7.409 18578 Z= 0.332 Chirality : 0.045 0.201 1990 Planarity : 0.005 0.038 2454 Dihedral : 7.026 114.888 1864 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.41 (0.20), residues: 1684 helix: -0.49 (0.20), residues: 656 sheet: -2.41 (0.30), residues: 220 loop : -2.31 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 523 HIS 0.004 0.001 HIS B 888 PHE 0.020 0.002 PHE A 624 TYR 0.024 0.002 TYR A 849 ARG 0.005 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.720 Fit side-chains REVERT: A 211 GLU cc_start: 0.6713 (pp20) cc_final: 0.6462 (pp20) REVERT: A 408 MET cc_start: 0.4815 (mmp) cc_final: 0.4206 (mmp) REVERT: A 492 GLU cc_start: 0.7960 (tt0) cc_final: 0.7717 (tt0) REVERT: B 101 PHE cc_start: 0.7269 (m-80) cc_final: 0.6749 (m-80) REVERT: B 173 MET cc_start: 0.7943 (tpp) cc_final: 0.6449 (tpp) REVERT: B 189 GLU cc_start: 0.4051 (tm-30) cc_final: 0.3751 (tm-30) REVERT: B 492 GLU cc_start: 0.7924 (tt0) cc_final: 0.7673 (tt0) REVERT: B 598 ASN cc_start: 0.8263 (p0) cc_final: 0.7973 (t0) REVERT: B 716 MET cc_start: 0.8785 (mmp) cc_final: 0.8543 (mmm) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2180 time to fit residues: 69.3435 Evaluate side-chains 148 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13722 Z= 0.260 Angle : 0.677 7.919 18578 Z= 0.335 Chirality : 0.046 0.185 1990 Planarity : 0.004 0.049 2454 Dihedral : 6.959 114.840 1864 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.41 (0.20), residues: 1684 helix: -0.51 (0.20), residues: 666 sheet: -2.25 (0.31), residues: 234 loop : -2.35 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 523 HIS 0.004 0.001 HIS A 888 PHE 0.021 0.002 PHE B 624 TYR 0.015 0.002 TYR B 99 ARG 0.006 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.605 Fit side-chains REVERT: A 211 GLU cc_start: 0.6816 (pp20) cc_final: 0.6614 (pp20) REVERT: A 408 MET cc_start: 0.4859 (mmp) cc_final: 0.4386 (mmp) REVERT: A 492 GLU cc_start: 0.7937 (tt0) cc_final: 0.7665 (tt0) REVERT: A 584 MET cc_start: 0.7369 (mtp) cc_final: 0.6734 (mtp) REVERT: A 716 MET cc_start: 0.8765 (mmp) cc_final: 0.8548 (mmm) REVERT: A 762 ARG cc_start: 0.7396 (mtm110) cc_final: 0.7166 (mtp-110) REVERT: B 173 MET cc_start: 0.8007 (tpp) cc_final: 0.6476 (tpp) REVERT: B 189 GLU cc_start: 0.3859 (tm-30) cc_final: 0.3555 (tm-30) REVERT: B 211 GLU cc_start: 0.6764 (pp20) cc_final: 0.6519 (pp20) REVERT: B 492 GLU cc_start: 0.7948 (tt0) cc_final: 0.7649 (tt0) REVERT: B 581 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7905 (ttm170) REVERT: B 762 ARG cc_start: 0.7394 (mtm110) cc_final: 0.7047 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2444 time to fit residues: 72.6393 Evaluate side-chains 148 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 HIS ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13722 Z= 0.165 Angle : 0.627 7.289 18578 Z= 0.307 Chirality : 0.044 0.157 1990 Planarity : 0.004 0.039 2454 Dihedral : 6.650 114.095 1864 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.10 (0.20), residues: 1684 helix: -0.26 (0.21), residues: 644 sheet: -2.12 (0.31), residues: 220 loop : -2.13 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 871 HIS 0.004 0.001 HIS B 174 PHE 0.020 0.001 PHE A 624 TYR 0.018 0.002 TYR B 99 ARG 0.004 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.665 Fit side-chains REVERT: A 408 MET cc_start: 0.4282 (mmp) cc_final: 0.3935 (mmp) REVERT: A 492 GLU cc_start: 0.7945 (tt0) cc_final: 0.7573 (tt0) REVERT: A 584 MET cc_start: 0.7343 (mtp) cc_final: 0.6798 (mtp) REVERT: A 716 MET cc_start: 0.8700 (mmp) cc_final: 0.8496 (mmm) REVERT: A 870 VAL cc_start: 0.8963 (p) cc_final: 0.8704 (m) REVERT: A 871 TRP cc_start: 0.8881 (t60) cc_final: 0.8234 (t60) REVERT: B 189 GLU cc_start: 0.3908 (tm-30) cc_final: 0.3569 (mm-30) REVERT: B 408 MET cc_start: 0.4420 (mmp) cc_final: 0.4095 (mmp) REVERT: B 492 GLU cc_start: 0.7958 (tt0) cc_final: 0.7608 (tt0) REVERT: B 584 MET cc_start: 0.7356 (mtp) cc_final: 0.6755 (mtp) REVERT: B 870 VAL cc_start: 0.8939 (p) cc_final: 0.8676 (m) REVERT: B 871 TRP cc_start: 0.8836 (t60) cc_final: 0.8229 (t60) REVERT: B 875 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7015 (mt-10) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2164 time to fit residues: 75.4721 Evaluate side-chains 161 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13722 Z= 0.277 Angle : 0.695 8.819 18578 Z= 0.343 Chirality : 0.046 0.170 1990 Planarity : 0.005 0.050 2454 Dihedral : 6.825 111.193 1864 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.20), residues: 1684 helix: -0.29 (0.20), residues: 662 sheet: -1.98 (0.34), residues: 194 loop : -2.17 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 523 HIS 0.005 0.001 HIS A 888 PHE 0.022 0.002 PHE B 624 TYR 0.026 0.002 TYR B 849 ARG 0.010 0.000 ARG B 763 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6853 (pp20) cc_final: 0.6615 (pp20) REVERT: A 271 LEU cc_start: 0.8356 (mp) cc_final: 0.7874 (tt) REVERT: A 324 GLU cc_start: 0.8309 (tp30) cc_final: 0.8101 (tp30) REVERT: A 408 MET cc_start: 0.4610 (mmp) cc_final: 0.4289 (mmp) REVERT: A 492 GLU cc_start: 0.7892 (tt0) cc_final: 0.7587 (tt0) REVERT: A 581 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7605 (ttm170) REVERT: A 584 MET cc_start: 0.7505 (mtp) cc_final: 0.6981 (mtp) REVERT: A 762 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7417 (mtp-110) REVERT: A 870 VAL cc_start: 0.9001 (p) cc_final: 0.8759 (m) REVERT: B 189 GLU cc_start: 0.3681 (tm-30) cc_final: 0.3305 (mm-30) REVERT: B 214 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7327 (mm-30) REVERT: B 408 MET cc_start: 0.4680 (mmp) cc_final: 0.4383 (mmp) REVERT: B 492 GLU cc_start: 0.7917 (tt0) cc_final: 0.7564 (tt0) REVERT: B 584 MET cc_start: 0.7533 (mtp) cc_final: 0.6881 (mtp) REVERT: B 870 VAL cc_start: 0.8986 (p) cc_final: 0.8732 (m) REVERT: B 875 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7282 (mt-10) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2300 time to fit residues: 69.2654 Evaluate side-chains 151 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.1980 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 0.3980 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13722 Z= 0.253 Angle : 0.680 8.220 18578 Z= 0.333 Chirality : 0.046 0.189 1990 Planarity : 0.005 0.043 2454 Dihedral : 6.750 107.650 1864 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.01 (0.20), residues: 1684 helix: -0.16 (0.21), residues: 650 sheet: -2.10 (0.33), residues: 194 loop : -2.12 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 523 HIS 0.004 0.001 HIS A 888 PHE 0.022 0.002 PHE A 624 TYR 0.020 0.002 TYR A 849 ARG 0.010 0.000 ARG A 763 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6873 (pp20) cc_final: 0.6605 (pp20) REVERT: A 271 LEU cc_start: 0.8361 (mp) cc_final: 0.7868 (tt) REVERT: A 408 MET cc_start: 0.4629 (mmp) cc_final: 0.4323 (mmp) REVERT: A 492 GLU cc_start: 0.7914 (tt0) cc_final: 0.7567 (tt0) REVERT: A 581 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7656 (ttm170) REVERT: A 584 MET cc_start: 0.7477 (mtp) cc_final: 0.7001 (mtp) REVERT: A 762 ARG cc_start: 0.7789 (mtp-110) cc_final: 0.7406 (mtp-110) REVERT: A 870 VAL cc_start: 0.8979 (p) cc_final: 0.8745 (m) REVERT: B 189 GLU cc_start: 0.3738 (tm-30) cc_final: 0.3340 (mm-30) REVERT: B 214 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7369 (mm-30) REVERT: B 408 MET cc_start: 0.4669 (mmp) cc_final: 0.4424 (mmp) REVERT: B 492 GLU cc_start: 0.7925 (tt0) cc_final: 0.7555 (tt0) REVERT: B 581 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7450 (ttm170) REVERT: B 584 MET cc_start: 0.7532 (mtp) cc_final: 0.6886 (mtp) REVERT: B 762 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.7490 (mtp-110) REVERT: B 870 VAL cc_start: 0.8969 (p) cc_final: 0.8717 (m) REVERT: B 875 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7316 (mt-10) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2330 time to fit residues: 70.6047 Evaluate side-chains 155 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 0.0010 chunk 137 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 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 = 0.3601 r_free = 0.3601 target = 0.119742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101572 restraints weight = 28037.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103329 restraints weight = 18601.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104772 restraints weight = 14151.336| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13722 Z= 0.245 Angle : 0.680 9.204 18578 Z= 0.333 Chirality : 0.046 0.165 1990 Planarity : 0.004 0.038 2454 Dihedral : 6.704 105.173 1864 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.00 (0.20), residues: 1684 helix: -0.13 (0.21), residues: 648 sheet: -2.10 (0.33), residues: 194 loop : -2.13 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 523 HIS 0.004 0.001 HIS B 720 PHE 0.022 0.002 PHE B 624 TYR 0.019 0.002 TYR A 849 ARG 0.010 0.000 ARG B 763 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.15 seconds wall clock time: 45 minutes 53.74 seconds (2753.74 seconds total)