Starting phenix.real_space_refine on Wed Feb 14 08:41:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crq_26955/02_2024/8crq_26955_updated.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= 0.122 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 6 5.49 5 S 38 5.16 5 C 5968 2.51 5 N 1408 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8936 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.80, per 1000 atoms: 0.54 Number of scatterers: 8936 At special positions: 0 Unit cell: (142.76, 80.925, 110.39, 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 38 16.00 P 6 15.00 O 1516 8.00 N 1408 7.00 C 5968 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 2 sheets defined 66.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'C' and resid 380 through 393 Proline residue: C 391 - end of helix Processing helix chain 'C' and resid 395 through 400 removed outlier: 5.209A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 430 removed outlier: 3.696A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 437 through 454 Processing helix chain 'C' and resid 466 through 482 Processing helix chain 'C' and resid 486 through 506 removed outlier: 3.563A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 Processing helix chain 'C' and resid 518 through 546 removed outlier: 3.657A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.678A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 661 through 689 removed outlier: 3.672A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA C 668 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU C 669 " --> pdb=" O PHE C 665 " (cutoff:3.500A) Proline residue: C 670 - end of helix Processing helix chain 'C' and resid 692 through 694 No H-bonds generated for 'chain 'C' and resid 692 through 694' Processing helix chain 'C' and resid 702 through 718 removed outlier: 3.723A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 Processing helix chain 'C' and resid 761 through 773 Processing helix chain 'C' and resid 777 through 782 removed outlier: 4.364A pdb=" N ARG C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 798 Processing helix chain 'C' and resid 804 through 813 removed outlier: 4.142A pdb=" N PHE C 813 " --> pdb=" O ILE C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 818 No H-bonds generated for 'chain 'C' and resid 816 through 818' Processing helix chain 'C' and resid 823 through 826 No H-bonds generated for 'chain 'C' and resid 823 through 826' Processing helix chain 'C' and resid 830 through 851 Processing helix chain 'C' and resid 856 through 871 Proline residue: C 860 - end of helix Proline residue: C 868 - end of helix Processing helix chain 'C' and resid 874 through 876 No H-bonds generated for 'chain 'C' and resid 874 through 876' Processing helix chain 'C' and resid 880 through 886 Processing helix chain 'E' and resid 380 through 392 Proline residue: E 391 - end of helix Processing helix chain 'E' and resid 395 through 400 removed outlier: 5.237A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 430 removed outlier: 3.613A pdb=" N PHE E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 437 through 454 Processing helix chain 'E' and resid 466 through 481 Processing helix chain 'E' and resid 486 through 506 removed outlier: 3.712A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.712A pdb=" N VAL E 513 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 546 removed outlier: 3.606A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 593 removed outlier: 3.716A pdb=" N ASN E 593 " --> pdb=" O ARG E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 609 through 622 Processing helix chain 'E' and resid 661 through 689 removed outlier: 3.546A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA E 668 " --> pdb=" O MET E 664 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU E 669 " --> pdb=" O PHE E 665 " (cutoff:3.500A) Proline residue: E 670 - end of helix Processing helix chain 'E' and resid 692 through 694 No H-bonds generated for 'chain 'E' and resid 692 through 694' Processing helix chain 'E' and resid 702 through 719 removed outlier: 3.594A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE E 719 " --> pdb=" O VAL E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 737 Processing helix chain 'E' and resid 761 through 774 removed outlier: 4.919A pdb=" N ILE E 774 " --> pdb=" O VAL E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 782 removed outlier: 4.202A pdb=" N ARG E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 800 removed outlier: 4.119A pdb=" N LEU E 800 " --> pdb=" O GLY E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 813 removed outlier: 3.563A pdb=" N LEU E 812 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE E 813 " --> pdb=" O ILE E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 818 No H-bonds generated for 'chain 'E' and resid 816 through 818' Processing helix chain 'E' and resid 823 through 826 No H-bonds generated for 'chain 'E' and resid 823 through 826' Processing helix chain 'E' and resid 830 through 851 Processing helix chain 'E' and resid 856 through 871 removed outlier: 3.704A pdb=" N LEU E 859 " --> pdb=" O SER E 856 " (cutoff:3.500A) Proline residue: E 860 - end of helix Proline residue: E 868 - end of helix removed outlier: 3.516A pdb=" N ARG E 871 " --> pdb=" O PRO E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 877 removed outlier: 3.584A pdb=" N ILE E 877 " --> pdb=" O LEU E 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 873 through 877' Processing helix chain 'E' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'C' and resid 739 through 741 Processing sheet with id= B, first strand: chain 'E' and resid 739 through 741 488 hydrogen bonds defined for protein. 1407 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: 2.59 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1310 1.31 - 1.43: 2435 1.43 - 1.56: 5335 1.56 - 1.68: 8 1.68 - 1.81: 70 Bond restraints: 9158 Sorted by residual: bond pdb=" C5 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C3 NAG F 2 " pdb=" O3 NAG F 2 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C VAL C 867 " pdb=" N PRO C 868 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.28e-02 6.10e+03 9.68e-01 bond pdb=" C3 NAG A 1 " pdb=" O3 NAG A 1 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.65e-01 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.91: 263 105.91 - 112.93: 5080 112.93 - 119.95: 3061 119.95 - 126.97: 3948 126.97 - 133.99: 110 Bond angle restraints: 12462 Sorted by residual: angle pdb=" C ARG C 389 " pdb=" N TYR C 390 " pdb=" CA TYR C 390 " ideal model delta sigma weight residual 120.06 123.56 -3.50 1.19e+00 7.06e-01 8.66e+00 angle pdb=" C THR E 866 " pdb=" N VAL E 867 " pdb=" CA VAL E 867 " ideal model delta sigma weight residual 120.33 122.42 -2.09 8.00e-01 1.56e+00 6.83e+00 angle pdb=" C ARG E 389 " pdb=" N TYR E 390 " pdb=" CA TYR E 390 " ideal model delta sigma weight residual 120.06 123.16 -3.10 1.19e+00 7.06e-01 6.80e+00 angle pdb=" N ILE D 114 " pdb=" CA ILE D 114 " pdb=" C ILE D 114 " ideal model delta sigma weight residual 110.21 107.65 2.56 1.13e+00 7.83e-01 5.12e+00 angle pdb=" N ASN C 569 " pdb=" CA ASN C 569 " pdb=" CB ASN C 569 " ideal model delta sigma weight residual 113.65 110.50 3.15 1.47e+00 4.63e-01 4.61e+00 ... (remaining 12457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.81: 5243 20.81 - 41.61: 204 41.61 - 62.41: 56 62.41 - 83.22: 9 83.22 - 104.02: 18 Dihedral angle restraints: 5530 sinusoidal: 2328 harmonic: 3202 Sorted by residual: dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" C5 NAG A 2 " ideal model delta sinusoidal sigma weight residual 53.78 -50.24 104.02 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" O4 NAG A 2 " ideal model delta sinusoidal sigma weight residual 175.11 71.48 103.63 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" C5 NAG F 2 " ideal model delta sinusoidal sigma weight residual 53.78 -49.72 103.50 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1065 0.041 - 0.082: 345 0.082 - 0.123: 88 0.123 - 0.164: 4 0.164 - 0.205: 2 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CB ILE E 487 " pdb=" CA ILE E 487 " pdb=" CG1 ILE E 487 " pdb=" CG2 ILE E 487 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 487 " pdb=" CA ILE C 487 " pdb=" CG1 ILE C 487 " pdb=" CG2 ILE C 487 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 642 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 1501 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 390 " -0.042 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO E 391 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 390 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO C 391 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 466 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO E 467 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 467 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 467 " -0.026 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 212 2.71 - 3.26: 9147 3.26 - 3.81: 14884 3.81 - 4.35: 18789 4.35 - 4.90: 31463 Nonbonded interactions: 74495 Sorted by model distance: nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.166 2.440 nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.222 2.440 nonbonded pdb=" O LEU E 427 " pdb=" OG1 THR E 431 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR C 393 " pdb=" O LEU C 453 " model vdw 2.304 2.440 nonbonded pdb=" O LEU C 863 " pdb=" OG1 THR C 866 " model vdw 2.310 2.440 ... (remaining 74490 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' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } 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: 3.120 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: 17.570 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.420 Find NCS groups from input model: 0.480 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.004 0.033 9158 Z= 0.228 Angle : 0.576 6.190 12462 Z= 0.309 Chirality : 0.042 0.205 1504 Planarity : 0.006 0.063 1494 Dihedral : 13.934 104.022 3466 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.37 % Allowed : 4.63 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.20 (0.24), residues: 1102 helix: 1.20 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.07 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.002 0.001 HIS B 85 PHE 0.013 0.001 PHE E 471 TYR 0.017 0.002 TYR C 519 ARG 0.003 0.001 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 1.099 Fit side-chains REVERT: B 92 ILE cc_start: 0.7136 (tp) cc_final: 0.6879 (tp) REVERT: C 487 ILE cc_start: 0.8281 (tp) cc_final: 0.7785 (tp) REVERT: C 646 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.6014 (ppp80) REVERT: C 693 GLU cc_start: 0.8381 (pm20) cc_final: 0.8160 (pm20) REVERT: C 757 LYS cc_start: 0.8474 (mmtp) cc_final: 0.8252 (mmtt) REVERT: C 782 ARG cc_start: 0.7842 (mtp85) cc_final: 0.6798 (ptt90) REVERT: C 827 ARG cc_start: 0.7075 (mtp85) cc_final: 0.6698 (mmm160) REVERT: E 511 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7801 (p90) REVERT: E 514 ARG cc_start: 0.8132 (ptm160) cc_final: 0.7906 (ptp-110) REVERT: E 589 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7758 (ttt90) REVERT: E 617 MET cc_start: 0.8229 (mmm) cc_final: 0.7917 (mmt) REVERT: E 621 ASP cc_start: 0.9119 (t70) cc_final: 0.8796 (t0) REVERT: E 646 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6855 (ppp80) REVERT: E 663 MET cc_start: 0.5526 (tpt) cc_final: 0.4561 (tpp) REVERT: E 782 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7699 (mpt180) outliers start: 13 outliers final: 5 residues processed: 211 average time/residue: 0.2941 time to fit residues: 82.1541 Evaluate side-chains 174 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 646 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN D 82 GLN C 377 GLN C 569 ASN C 630 GLN C 683 GLN E 377 GLN E 564 GLN E 630 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9158 Z= 0.169 Angle : 0.518 7.177 12462 Z= 0.250 Chirality : 0.041 0.207 1504 Planarity : 0.005 0.057 1494 Dihedral : 12.107 88.970 1473 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.11 % Allowed : 8.95 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.78 (0.25), residues: 1102 helix: 1.71 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.09 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 492 HIS 0.001 0.000 HIS C 651 PHE 0.024 0.001 PHE E 476 TYR 0.016 0.001 TYR C 519 ARG 0.005 0.001 ARG C 656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 0.989 Fit side-chains REVERT: B 92 ILE cc_start: 0.7100 (tp) cc_final: 0.6830 (tp) REVERT: C 646 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.5881 (ppp80) REVERT: C 693 GLU cc_start: 0.8387 (pm20) cc_final: 0.8129 (pm20) REVERT: C 782 ARG cc_start: 0.7875 (mtp85) cc_final: 0.6777 (ptt90) REVERT: C 827 ARG cc_start: 0.7086 (mtp85) cc_final: 0.6674 (mmm160) REVERT: E 511 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7715 (p90) REVERT: E 514 ARG cc_start: 0.8213 (ptm160) cc_final: 0.7872 (ptp-110) REVERT: E 589 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7678 (ttt90) REVERT: E 593 ASN cc_start: 0.8169 (m110) cc_final: 0.7924 (m110) REVERT: E 621 ASP cc_start: 0.9172 (t70) cc_final: 0.8870 (t0) REVERT: E 663 MET cc_start: 0.5353 (tpt) cc_final: 0.4358 (tpp) REVERT: E 676 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7991 (mp) REVERT: E 782 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7668 (mpt180) outliers start: 20 outliers final: 15 residues processed: 183 average time/residue: 0.2404 time to fit residues: 58.6771 Evaluate side-chains 185 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 849 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0670 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 569 ASN C 819 HIS E 651 HIS E 819 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9158 Z= 0.126 Angle : 0.472 6.555 12462 Z= 0.229 Chirality : 0.039 0.175 1504 Planarity : 0.005 0.054 1494 Dihedral : 9.655 89.089 1473 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.32 % Allowed : 10.74 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.99 (0.25), residues: 1102 helix: 1.92 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.02 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 492 HIS 0.001 0.000 HIS C 834 PHE 0.023 0.001 PHE E 476 TYR 0.017 0.001 TYR E 486 ARG 0.005 0.000 ARG E 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 0.995 Fit side-chains REVERT: B 83 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7268 (tt) REVERT: B 92 ILE cc_start: 0.7111 (tp) cc_final: 0.6837 (tp) REVERT: C 384 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6419 (ttp-110) REVERT: C 646 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.5909 (ppp80) REVERT: C 693 GLU cc_start: 0.8371 (pm20) cc_final: 0.8105 (pm20) REVERT: C 782 ARG cc_start: 0.7893 (mtp85) cc_final: 0.6746 (ptt90) REVERT: C 827 ARG cc_start: 0.7100 (mtp85) cc_final: 0.6681 (mmm160) REVERT: E 394 LEU cc_start: 0.6977 (tp) cc_final: 0.6410 (tp) REVERT: E 511 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7682 (p90) REVERT: E 514 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7723 (ptp-110) REVERT: E 589 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7670 (ttt90) REVERT: E 593 ASN cc_start: 0.8168 (m110) cc_final: 0.7938 (m110) REVERT: E 617 MET cc_start: 0.7909 (mmt) cc_final: 0.7698 (mmt) REVERT: E 621 ASP cc_start: 0.9209 (t70) cc_final: 0.8893 (t0) REVERT: E 646 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.5242 (ppp80) REVERT: E 663 MET cc_start: 0.5255 (tpt) cc_final: 0.4257 (tpp) REVERT: E 676 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7992 (mp) REVERT: E 782 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7622 (mpt180) outliers start: 22 outliers final: 9 residues processed: 185 average time/residue: 0.2432 time to fit residues: 60.0506 Evaluate side-chains 177 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9158 Z= 0.176 Angle : 0.484 8.836 12462 Z= 0.235 Chirality : 0.040 0.157 1504 Planarity : 0.005 0.053 1494 Dihedral : 8.699 80.585 1469 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.63 % Allowed : 12.11 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.02 (0.25), residues: 1102 helix: 1.91 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.13 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.001 0.000 HIS E 734 PHE 0.013 0.001 PHE C 471 TYR 0.016 0.001 TYR C 519 ARG 0.005 0.000 ARG E 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.011 Fit side-chains REVERT: B 83 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7279 (tt) REVERT: B 92 ILE cc_start: 0.7046 (tp) cc_final: 0.6737 (tp) REVERT: C 384 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6450 (ttp-110) REVERT: C 607 ASP cc_start: 0.7173 (m-30) cc_final: 0.6954 (m-30) REVERT: C 646 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.5873 (ppp80) REVERT: C 650 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8428 (mp) REVERT: C 693 GLU cc_start: 0.8405 (pm20) cc_final: 0.8122 (pm20) REVERT: C 782 ARG cc_start: 0.7927 (mtp85) cc_final: 0.6745 (ptt90) REVERT: C 827 ARG cc_start: 0.7144 (mtp85) cc_final: 0.6693 (mmm160) REVERT: E 394 LEU cc_start: 0.6989 (tp) cc_final: 0.6418 (tp) REVERT: E 511 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7702 (p90) REVERT: E 589 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7666 (ttt90) REVERT: E 593 ASN cc_start: 0.8159 (m110) cc_final: 0.7946 (m110) REVERT: E 621 ASP cc_start: 0.9225 (t70) cc_final: 0.8932 (t0) REVERT: E 646 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.5469 (ppp80) REVERT: E 650 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7175 (mp) REVERT: E 658 GLU cc_start: 0.7267 (tp30) cc_final: 0.6690 (mp0) REVERT: E 663 MET cc_start: 0.5241 (tpt) cc_final: 0.4231 (tpp) REVERT: E 676 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.8020 (mp) REVERT: E 782 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7634 (mpt180) outliers start: 25 outliers final: 13 residues processed: 189 average time/residue: 0.2299 time to fit residues: 58.3129 Evaluate side-chains 188 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9158 Z= 0.153 Angle : 0.463 7.552 12462 Z= 0.227 Chirality : 0.040 0.183 1504 Planarity : 0.005 0.053 1494 Dihedral : 8.355 74.838 1469 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.95 % Allowed : 12.53 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1102 helix: 2.03 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.05 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 492 HIS 0.001 0.000 HIS E 651 PHE 0.014 0.001 PHE C 471 TYR 0.015 0.001 TYR C 519 ARG 0.008 0.000 ARG E 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 0.943 Fit side-chains REVERT: B 83 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7226 (tt) REVERT: B 92 ILE cc_start: 0.7053 (tp) cc_final: 0.6741 (tp) REVERT: C 499 LEU cc_start: 0.7826 (tp) cc_final: 0.7446 (tt) REVERT: C 607 ASP cc_start: 0.7191 (m-30) cc_final: 0.6956 (m-30) REVERT: C 646 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.5849 (ppp80) REVERT: C 650 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 693 GLU cc_start: 0.8407 (pm20) cc_final: 0.8118 (pm20) REVERT: C 782 ARG cc_start: 0.7937 (mtp85) cc_final: 0.6731 (ptt90) REVERT: C 827 ARG cc_start: 0.7169 (mtp85) cc_final: 0.6705 (mmm160) REVERT: E 394 LEU cc_start: 0.6953 (tp) cc_final: 0.6388 (tp) REVERT: E 511 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7699 (p90) REVERT: E 589 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7662 (ttt90) REVERT: E 593 ASN cc_start: 0.8146 (m110) cc_final: 0.7933 (m110) REVERT: E 621 ASP cc_start: 0.9228 (t70) cc_final: 0.8947 (t0) REVERT: E 650 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7624 (mp) REVERT: E 658 GLU cc_start: 0.7283 (tp30) cc_final: 0.6690 (mp0) REVERT: E 663 MET cc_start: 0.5222 (tpt) cc_final: 0.4214 (tpp) REVERT: E 782 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7621 (mpt180) outliers start: 28 outliers final: 15 residues processed: 187 average time/residue: 0.2378 time to fit residues: 59.7623 Evaluate side-chains 184 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 487 ILE Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.8137 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9158 Z= 0.331 Angle : 0.583 7.167 12462 Z= 0.286 Chirality : 0.044 0.186 1504 Planarity : 0.005 0.054 1494 Dihedral : 8.533 74.039 1469 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.05 % Allowed : 12.84 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.48 (0.25), residues: 1102 helix: 1.59 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 492 HIS 0.002 0.001 HIS E 734 PHE 0.015 0.002 PHE E 836 TYR 0.023 0.002 TYR C 519 ARG 0.008 0.001 ARG C 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 0.979 Fit side-chains REVERT: B 83 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7224 (tt) REVERT: B 92 ILE cc_start: 0.7168 (tp) cc_final: 0.6864 (tp) REVERT: C 487 ILE cc_start: 0.8425 (tp) cc_final: 0.7900 (tp) REVERT: C 499 LEU cc_start: 0.7953 (tp) cc_final: 0.7608 (tt) REVERT: C 607 ASP cc_start: 0.7222 (m-30) cc_final: 0.6921 (m-30) REVERT: C 646 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.5832 (ppp80) REVERT: C 650 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8443 (mp) REVERT: C 693 GLU cc_start: 0.8499 (pm20) cc_final: 0.8225 (pm20) REVERT: C 782 ARG cc_start: 0.7970 (mtp85) cc_final: 0.6770 (ptt90) REVERT: E 511 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7793 (p90) REVERT: E 562 LYS cc_start: 0.7097 (ptmm) cc_final: 0.6622 (pttm) REVERT: E 589 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7680 (ttt90) REVERT: E 593 ASN cc_start: 0.8152 (m110) cc_final: 0.7945 (m110) REVERT: E 621 ASP cc_start: 0.9243 (t70) cc_final: 0.8964 (t0) REVERT: E 646 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.5905 (ppp80) REVERT: E 658 GLU cc_start: 0.7340 (tp30) cc_final: 0.6686 (mp0) REVERT: E 663 MET cc_start: 0.5294 (tpt) cc_final: 0.3565 (tpp) REVERT: E 782 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7683 (mpt180) outliers start: 29 outliers final: 17 residues processed: 188 average time/residue: 0.2425 time to fit residues: 61.1887 Evaluate side-chains 190 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 487 ILE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 849 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9158 Z= 0.256 Angle : 0.528 9.672 12462 Z= 0.259 Chirality : 0.042 0.175 1504 Planarity : 0.005 0.055 1494 Dihedral : 8.443 76.132 1469 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.95 % Allowed : 13.26 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.53 (0.25), residues: 1102 helix: 1.66 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.31 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 492 HIS 0.002 0.001 HIS E 651 PHE 0.014 0.001 PHE C 471 TYR 0.019 0.002 TYR C 519 ARG 0.008 0.001 ARG C 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.037 Fit side-chains REVERT: B 83 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7200 (tt) REVERT: B 92 ILE cc_start: 0.7163 (tp) cc_final: 0.6860 (tp) REVERT: C 430 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8159 (ttmt) REVERT: C 499 LEU cc_start: 0.7910 (tp) cc_final: 0.7548 (tt) REVERT: C 607 ASP cc_start: 0.7218 (m-30) cc_final: 0.6931 (m-30) REVERT: C 646 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.5940 (ppp80) REVERT: C 693 GLU cc_start: 0.8473 (pm20) cc_final: 0.8205 (pm20) REVERT: C 782 ARG cc_start: 0.7958 (mtp85) cc_final: 0.6757 (ptt90) REVERT: C 827 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6766 (mtp-110) REVERT: E 511 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7796 (p90) REVERT: E 589 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7679 (ttt90) REVERT: E 593 ASN cc_start: 0.8143 (m110) cc_final: 0.7930 (m110) REVERT: E 621 ASP cc_start: 0.9243 (t70) cc_final: 0.8955 (t0) REVERT: E 646 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.5702 (ppp80) REVERT: E 650 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7330 (mp) REVERT: E 658 GLU cc_start: 0.7375 (tp30) cc_final: 0.6690 (mp0) REVERT: E 663 MET cc_start: 0.5298 (tpt) cc_final: 0.3875 (tpt) REVERT: E 782 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7663 (mpt180) outliers start: 28 outliers final: 18 residues processed: 190 average time/residue: 0.2365 time to fit residues: 60.3066 Evaluate side-chains 194 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 487 ILE Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 849 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 0.0170 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9158 Z= 0.169 Angle : 0.489 9.247 12462 Z= 0.240 Chirality : 0.040 0.156 1504 Planarity : 0.005 0.056 1494 Dihedral : 8.173 78.818 1469 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.63 % Allowed : 14.21 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.83 (0.25), residues: 1102 helix: 1.90 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.18 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 492 HIS 0.001 0.000 HIS E 651 PHE 0.015 0.001 PHE C 471 TYR 0.015 0.001 TYR C 519 ARG 0.008 0.000 ARG E 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 0.972 Fit side-chains REVERT: B 83 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7174 (tt) REVERT: B 92 ILE cc_start: 0.7090 (tp) cc_final: 0.6773 (tp) REVERT: C 430 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8147 (ttmt) REVERT: C 499 LEU cc_start: 0.7852 (tp) cc_final: 0.7461 (tt) REVERT: C 607 ASP cc_start: 0.7203 (m-30) cc_final: 0.6950 (m-30) REVERT: C 646 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.5928 (ppp80) REVERT: C 693 GLU cc_start: 0.8436 (pm20) cc_final: 0.8165 (pm20) REVERT: C 782 ARG cc_start: 0.7952 (mtp85) cc_final: 0.6743 (ptt90) REVERT: C 827 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6647 (mmm160) REVERT: E 394 LEU cc_start: 0.6953 (tp) cc_final: 0.6373 (tp) REVERT: E 511 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7736 (p90) REVERT: E 589 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7682 (ttt90) REVERT: E 621 ASP cc_start: 0.9234 (t70) cc_final: 0.8945 (t0) REVERT: E 646 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.5530 (ppp80) REVERT: E 650 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7157 (mp) REVERT: E 658 GLU cc_start: 0.7356 (tp30) cc_final: 0.6650 (mp0) REVERT: E 663 MET cc_start: 0.5303 (tpt) cc_final: 0.3569 (tpp) REVERT: E 782 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7632 (mpt180) outliers start: 25 outliers final: 16 residues processed: 189 average time/residue: 0.2365 time to fit residues: 60.2170 Evaluate side-chains 193 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 487 ILE Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 GLN E 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9158 Z= 0.158 Angle : 0.485 9.096 12462 Z= 0.237 Chirality : 0.040 0.149 1504 Planarity : 0.005 0.055 1494 Dihedral : 8.000 78.648 1469 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.63 % Allowed : 14.53 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.97 (0.25), residues: 1102 helix: 2.01 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.11 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 492 HIS 0.001 0.000 HIS E 651 PHE 0.015 0.001 PHE C 471 TYR 0.014 0.001 TYR C 519 ARG 0.009 0.000 ARG C 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.085 Fit side-chains REVERT: B 83 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7136 (tt) REVERT: B 92 ILE cc_start: 0.7073 (tp) cc_final: 0.6754 (tp) REVERT: C 499 LEU cc_start: 0.7819 (tp) cc_final: 0.7415 (tt) REVERT: C 607 ASP cc_start: 0.7205 (m-30) cc_final: 0.6944 (m-30) REVERT: C 646 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.5922 (ppp80) REVERT: C 693 GLU cc_start: 0.8446 (pm20) cc_final: 0.8176 (pm20) REVERT: C 782 ARG cc_start: 0.7946 (mtp85) cc_final: 0.6722 (ptt90) REVERT: C 827 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6621 (mmm160) REVERT: E 394 LEU cc_start: 0.6971 (tp) cc_final: 0.6411 (tp) REVERT: E 511 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7716 (p90) REVERT: E 515 PHE cc_start: 0.7746 (m-80) cc_final: 0.7541 (m-80) REVERT: E 589 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7723 (ttt90) REVERT: E 646 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.5771 (ppp80) REVERT: E 658 GLU cc_start: 0.7341 (tp30) cc_final: 0.6637 (mp0) REVERT: E 663 MET cc_start: 0.5270 (tpt) cc_final: 0.3536 (tpp) REVERT: E 680 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8024 (mt) REVERT: E 754 GLN cc_start: 0.7137 (tp40) cc_final: 0.6881 (tp40) REVERT: E 782 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7599 (mpt180) outliers start: 25 outliers final: 16 residues processed: 184 average time/residue: 0.2376 time to fit residues: 58.4889 Evaluate side-chains 189 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 487 ILE Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.0170 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 67 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9158 Z= 0.234 Angle : 0.528 9.051 12462 Z= 0.258 Chirality : 0.041 0.164 1504 Planarity : 0.005 0.055 1494 Dihedral : 8.086 75.646 1469 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.53 % Allowed : 14.84 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.67 (0.25), residues: 1102 helix: 1.76 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.28 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 492 HIS 0.002 0.001 HIS D 85 PHE 0.014 0.001 PHE C 471 TYR 0.019 0.001 TYR C 519 ARG 0.008 0.001 ARG C 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.011 Fit side-chains REVERT: B 83 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7153 (tt) REVERT: B 92 ILE cc_start: 0.7131 (tp) cc_final: 0.6814 (tp) REVERT: C 499 LEU cc_start: 0.7870 (tp) cc_final: 0.7481 (tt) REVERT: C 607 ASP cc_start: 0.7211 (m-30) cc_final: 0.6924 (m-30) REVERT: C 646 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.6006 (ppp80) REVERT: C 693 GLU cc_start: 0.8475 (pm20) cc_final: 0.8200 (pm20) REVERT: C 782 ARG cc_start: 0.7969 (mtp85) cc_final: 0.6761 (ptt90) REVERT: C 827 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6652 (mmm160) REVERT: E 394 LEU cc_start: 0.6974 (tp) cc_final: 0.6411 (tp) REVERT: E 511 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7789 (p90) REVERT: E 589 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7726 (ttt90) REVERT: E 621 ASP cc_start: 0.9244 (t70) cc_final: 0.8960 (t0) REVERT: E 646 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.5943 (ppp80) REVERT: E 658 GLU cc_start: 0.7380 (tp30) cc_final: 0.6646 (mp0) REVERT: E 663 MET cc_start: 0.5286 (tpt) cc_final: 0.3856 (tpt) REVERT: E 782 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7662 (mpt180) outliers start: 24 outliers final: 17 residues processed: 184 average time/residue: 0.2412 time to fit residues: 59.4634 Evaluate side-chains 190 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 487 ILE Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 703 HIS E 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.152250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.127993 restraints weight = 10459.269| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.49 r_work: 0.3228 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9158 Z= 0.162 Angle : 0.490 9.905 12462 Z= 0.239 Chirality : 0.040 0.151 1504 Planarity : 0.005 0.055 1494 Dihedral : 7.926 75.506 1469 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.53 % Allowed : 14.84 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.92 (0.25), residues: 1102 helix: 1.98 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.16 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 492 HIS 0.001 0.000 HIS E 651 PHE 0.015 0.001 PHE C 471 TYR 0.015 0.001 TYR C 519 ARG 0.008 0.000 ARG C 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.30 seconds wall clock time: 45 minutes 43.08 seconds (2743.08 seconds total)