Starting phenix.real_space_refine on Thu Jan 18 15:22:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crr_26956/01_2024/8crr_26956_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.154 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 "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 638": "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 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 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 679": "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" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 5.52, per 1000 atoms: 0.62 Number of scatterers: 8936 At special positions: 0 Unit cell: (104.165, 109.145, 126.575, 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: 3.92 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 3 sheets defined 66.7% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 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 392 Proline residue: C 391 - end of helix Processing helix chain 'C' and resid 395 through 400 removed outlier: 4.866A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 430 removed outlier: 3.657A 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 481 Processing helix chain 'C' and resid 486 through 506 removed outlier: 3.620A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.504A pdb=" N VAL C 513 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 546 removed outlier: 3.601A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.747A 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: 3.596A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA C 668 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 5.086A 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 719 removed outlier: 3.755A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE C 719 " --> pdb=" O VAL C 715 " (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: 4.579A pdb=" N ARG C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 800 removed outlier: 3.975A pdb=" N LEU C 800 " --> pdb=" O GLY C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 813 removed outlier: 3.513A pdb=" N LEU C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) removed outlier: 4.096A 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 removed outlier: 3.535A pdb=" N LEU C 859 " --> pdb=" O SER C 856 " (cutoff:3.500A) 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: 5.114A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 430 removed outlier: 3.685A 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 482 Processing helix chain 'E' and resid 486 through 506 removed outlier: 3.606A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.686A pdb=" N VAL E 513 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 546 removed outlier: 3.538A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 593 removed outlier: 3.706A 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: 3.510A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA E 668 " --> pdb=" O MET E 664 " (cutoff:3.500A) removed outlier: 5.180A 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: 3.661A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.748A 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 773 Processing helix chain 'E' and resid 777 through 782 removed outlier: 4.271A pdb=" N ARG E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 800 removed outlier: 3.962A pdb=" N LEU E 800 " --> pdb=" O GLY E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 813 removed outlier: 4.134A 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 Proline residue: E 860 - end of helix Proline residue: E 868 - end of helix Processing helix chain 'E' and resid 873 through 877 removed outlier: 3.764A 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 461 through 463 removed outlier: 4.957A pdb=" N VAL C 461 " --> pdb=" O THR C 727 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 739 through 741 Processing sheet with id= C, first strand: chain 'E' and resid 739 through 741 492 hydrogen bonds defined for protein. 1416 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: 2.52 Time building geometry restraints manager: 4.15 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: 2439 1.43 - 1.56: 5331 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 1.19e+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 1.12e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.433 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C3 NAG A 2 " pdb=" O3 NAG A 2 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.02: 210 105.02 - 112.27: 4845 112.27 - 119.51: 2895 119.51 - 126.75: 4388 126.75 - 134.00: 124 Bond angle restraints: 12462 Sorted by residual: angle pdb=" N ASN E 569 " pdb=" CA ASN E 569 " pdb=" CB ASN E 569 " ideal model delta sigma weight residual 113.65 110.15 3.50 1.47e+00 4.63e-01 5.66e+00 angle pdb=" N TYR E 390 " pdb=" CA TYR E 390 " pdb=" C TYR E 390 " ideal model delta sigma weight residual 109.81 114.85 -5.04 2.21e+00 2.05e-01 5.20e+00 angle pdb=" C1A PIO C1002 " pdb=" O2C PIO C1002 " pdb=" C2C PIO C1002 " ideal model delta sigma weight residual 113.89 119.55 -5.66 3.00e+00 1.11e-01 3.56e+00 angle pdb=" CA TRP C 492 " pdb=" CB TRP C 492 " pdb=" CG TRP C 492 " ideal model delta sigma weight residual 113.60 110.13 3.47 1.90e+00 2.77e-01 3.34e+00 angle pdb=" C TYR E 596 " pdb=" N PHE E 597 " pdb=" CA PHE E 597 " ideal model delta sigma weight residual 121.80 126.22 -4.42 2.44e+00 1.68e-01 3.28e+00 ... (remaining 12457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 5247 21.47 - 42.94: 210 42.94 - 64.42: 41 64.42 - 85.89: 15 85.89 - 107.36: 17 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 -53.58 107.36 1 3.00e+01 1.11e-03 1.38e+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 67.84 107.27 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C5 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" O3 NAG A 2 " ideal model delta sinusoidal sigma weight residual -174.13 -67.97 -106.16 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 930 0.034 - 0.068: 402 0.068 - 0.103: 125 0.103 - 0.137: 45 0.137 - 0.171: 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 2.47 0.17 2.00e-01 2.50e+01 7.30e-01 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 2.49 0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA LEU C 874 " pdb=" N LEU C 874 " pdb=" C LEU C 874 " pdb=" CB LEU C 874 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1501 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 390 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO E 391 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " 0.037 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 6.12e-02 6.00e+00 pdb=" N PRO C 391 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 466 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO E 467 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 467 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 467 " -0.025 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 359 2.72 - 3.27: 9243 3.27 - 3.81: 15213 3.81 - 4.36: 18809 4.36 - 4.90: 31576 Nonbonded interactions: 75200 Sorted by model distance: nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.180 2.440 nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.192 2.440 nonbonded pdb=" O PRO C 548 " pdb=" OH TYR C 553 " model vdw 2.268 2.440 nonbonded pdb=" NH2 ARG C 694 " pdb=" OD1 ASN C 736 " model vdw 2.291 2.520 nonbonded pdb=" O LEU C 863 " pdb=" OG1 THR C 866 " model vdw 2.317 2.440 ... (remaining 75195 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: 2.350 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: 0.020 Extract box with map and model: 11.120 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.520 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 0.039 9158 Z= 0.270 Angle : 0.583 6.096 12462 Z= 0.302 Chirality : 0.043 0.171 1504 Planarity : 0.006 0.066 1494 Dihedral : 14.251 107.362 3466 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.95 % Allowed : 5.16 % Favored : 93.89 % 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: 1.34 (0.24), residues: 1102 helix: 1.29 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.21 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 492 HIS 0.002 0.000 HIS E 651 PHE 0.016 0.001 PHE E 471 TYR 0.015 0.002 TYR E 392 ARG 0.002 0.000 ARG E 388 *********************** 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 228 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 219 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 426 LEU cc_start: 0.8879 (mt) cc_final: 0.8585 (mm) REVERT: C 472 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8223 (mm-30) REVERT: C 473 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: C 646 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.5948 (ppp80) REVERT: C 656 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.6883 (mtt180) REVERT: C 807 ASP cc_start: 0.8384 (m-30) cc_final: 0.8096 (m-30) REVERT: E 691 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7726 (mttm) REVERT: E 807 ASP cc_start: 0.8351 (m-30) cc_final: 0.8102 (m-30) outliers start: 9 outliers final: 2 residues processed: 223 average time/residue: 1.2218 time to fit residues: 290.3909 Evaluate side-chains 179 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 473 GLU 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: 2.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 GLN C 377 GLN C 457 GLN C 482 ASN C 564 GLN C 630 GLN ** C 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 GLN C 819 HIS E 377 GLN E 550 GLN ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN E 683 GLN E 759 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9158 Z= 0.288 Angle : 0.566 6.834 12462 Z= 0.277 Chirality : 0.043 0.201 1504 Planarity : 0.006 0.063 1494 Dihedral : 12.081 84.530 1470 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.74 % Allowed : 10.84 % Favored : 86.42 % 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: 1.60 (0.24), residues: 1102 helix: 1.51 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.25 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS B 86 PHE 0.018 0.001 PHE E 471 TYR 0.020 0.002 TYR C 824 ARG 0.006 0.001 ARG E 827 *********************** 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 218 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.031 Fit side-chains REVERT: C 384 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7412 (mtt180) REVERT: C 426 LEU cc_start: 0.8898 (mt) cc_final: 0.8614 (mm) REVERT: C 472 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8261 (mm-30) REVERT: C 473 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: C 646 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.5797 (ppp80) REVERT: C 656 ARG cc_start: 0.7877 (mmt-90) cc_final: 0.6936 (mtt180) REVERT: C 807 ASP cc_start: 0.8329 (m-30) cc_final: 0.8004 (m-30) REVERT: E 399 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: E 429 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7611 (mm-30) REVERT: E 535 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8124 (mp0) REVERT: E 681 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: E 691 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7521 (mttm) REVERT: E 807 ASP cc_start: 0.8314 (m-30) cc_final: 0.8066 (m-30) REVERT: E 879 ARG cc_start: 0.7663 (mmp-170) cc_final: 0.6807 (mtt90) outliers start: 26 outliers final: 12 residues processed: 201 average time/residue: 1.1841 time to fit residues: 254.8202 Evaluate side-chains 202 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 877 ILE Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** C 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN E 564 GLN E 703 HIS E 759 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9158 Z= 0.157 Angle : 0.487 7.456 12462 Z= 0.238 Chirality : 0.040 0.148 1504 Planarity : 0.005 0.059 1494 Dihedral : 9.461 87.500 1467 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.53 % Allowed : 12.63 % Favored : 84.84 % 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: 1.86 (0.24), residues: 1102 helix: 1.76 (0.18), residues: 752 sheet: None (None), residues: 0 loop : 0.18 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 PHE 0.015 0.001 PHE C 511 TYR 0.016 0.001 TYR C 824 ARG 0.007 0.000 ARG E 827 *********************** 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 211 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7802 (mmt180) cc_final: 0.7396 (mtt180) REVERT: C 426 LEU cc_start: 0.8871 (mt) cc_final: 0.8649 (mm) REVERT: C 472 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8212 (mm-30) REVERT: C 473 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: C 646 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.5895 (ppp80) REVERT: C 656 ARG cc_start: 0.7847 (mmt-90) cc_final: 0.6907 (mtt180) REVERT: C 696 MET cc_start: 0.8719 (mmt) cc_final: 0.8478 (mmt) REVERT: C 807 ASP cc_start: 0.8302 (m-30) cc_final: 0.8030 (m-30) REVERT: C 817 LYS cc_start: 0.8975 (pttt) cc_final: 0.8757 (pttp) REVERT: C 835 LEU cc_start: 0.8907 (tp) cc_final: 0.8587 (tt) REVERT: C 844 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8410 (tt) REVERT: E 429 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7577 (mm-30) REVERT: E 535 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8061 (mp0) REVERT: E 807 ASP cc_start: 0.8282 (m-30) cc_final: 0.8026 (m-30) REVERT: E 879 ARG cc_start: 0.7611 (mmp-170) cc_final: 0.6741 (mtt90) outliers start: 24 outliers final: 11 residues processed: 198 average time/residue: 1.1698 time to fit residues: 248.0474 Evaluate side-chains 191 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 864 ILE Chi-restraints excluded: chain E residue 877 ILE 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: 5.9990 chunk 51 optimal weight: 0.0970 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 651 HIS E 759 GLN E 819 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9158 Z= 0.137 Angle : 0.458 5.841 12462 Z= 0.228 Chirality : 0.039 0.163 1504 Planarity : 0.005 0.059 1494 Dihedral : 8.556 89.617 1467 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.84 % Allowed : 14.42 % Favored : 82.74 % 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: 2.08 (0.25), residues: 1102 helix: 1.94 (0.19), residues: 752 sheet: None (None), residues: 0 loop : 0.23 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 492 HIS 0.001 0.000 HIS E 703 PHE 0.015 0.001 PHE C 511 TYR 0.014 0.001 TYR C 824 ARG 0.005 0.000 ARG E 514 *********************** 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 211 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7391 (mtt180) REVERT: C 426 LEU cc_start: 0.8870 (mt) cc_final: 0.8651 (mm) REVERT: C 472 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8177 (mm-30) REVERT: C 473 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: C 646 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.6060 (ppp80) REVERT: C 656 ARG cc_start: 0.7831 (mmt-90) cc_final: 0.6896 (mtt180) REVERT: C 807 ASP cc_start: 0.8286 (m-30) cc_final: 0.8042 (m-30) REVERT: C 835 LEU cc_start: 0.8839 (tp) cc_final: 0.8490 (tt) REVERT: E 429 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7548 (mm-30) REVERT: E 535 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8026 (mp0) REVERT: E 564 GLN cc_start: 0.8602 (mm110) cc_final: 0.8298 (mp10) REVERT: E 807 ASP cc_start: 0.8299 (m-30) cc_final: 0.8048 (m-30) REVERT: E 879 ARG cc_start: 0.7597 (mmp-170) cc_final: 0.6716 (mtt90) outliers start: 27 outliers final: 12 residues processed: 197 average time/residue: 1.1248 time to fit residues: 237.9483 Evaluate side-chains 197 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 864 ILE 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: 5.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 759 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9158 Z= 0.179 Angle : 0.471 6.021 12462 Z= 0.233 Chirality : 0.040 0.149 1504 Planarity : 0.005 0.058 1494 Dihedral : 8.378 87.690 1467 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.26 % Allowed : 14.42 % Favored : 82.32 % 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: 2.10 (0.25), residues: 1102 helix: 1.98 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.20 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 PHE 0.017 0.001 PHE C 511 TYR 0.014 0.001 TYR C 824 ARG 0.004 0.000 ARG E 514 *********************** 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 218 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7810 (mmt180) cc_final: 0.7427 (mtt180) REVERT: C 426 LEU cc_start: 0.8868 (mt) cc_final: 0.8651 (mm) REVERT: C 472 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8190 (mm-30) REVERT: C 473 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: C 646 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.5986 (ppp80) REVERT: C 656 ARG cc_start: 0.7851 (mmt-90) cc_final: 0.6916 (mtt180) REVERT: C 807 ASP cc_start: 0.8306 (m-30) cc_final: 0.8046 (m-30) REVERT: C 833 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8389 (ttp) REVERT: C 835 LEU cc_start: 0.8899 (tp) cc_final: 0.8559 (tt) REVERT: E 429 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7541 (mm-30) REVERT: E 535 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8015 (mp0) REVERT: E 564 GLN cc_start: 0.8654 (mm110) cc_final: 0.8375 (mp10) REVERT: E 656 ARG cc_start: 0.7355 (mmt-90) cc_final: 0.7103 (mtt180) REVERT: E 807 ASP cc_start: 0.8341 (m-30) cc_final: 0.8091 (m-30) REVERT: E 851 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7740 (ttpp) REVERT: E 879 ARG cc_start: 0.7623 (mmp-170) cc_final: 0.6708 (mtt90) outliers start: 31 outliers final: 17 residues processed: 202 average time/residue: 1.1348 time to fit residues: 245.7398 Evaluate side-chains 204 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 833 MET Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 759 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9158 Z= 0.170 Angle : 0.466 6.018 12462 Z= 0.232 Chirality : 0.040 0.184 1504 Planarity : 0.005 0.058 1494 Dihedral : 8.226 85.348 1467 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.95 % Allowed : 14.84 % Favored : 82.21 % 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: 2.10 (0.25), residues: 1102 helix: 1.98 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.20 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 PHE 0.016 0.001 PHE C 511 TYR 0.015 0.001 TYR C 824 ARG 0.005 0.000 ARG C 603 *********************** 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 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7809 (mmt180) cc_final: 0.7410 (mtt180) REVERT: C 426 LEU cc_start: 0.8856 (mt) cc_final: 0.8638 (mm) REVERT: C 472 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8237 (mm-30) REVERT: C 473 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: C 646 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.5859 (ppp80) REVERT: C 656 ARG cc_start: 0.7873 (mmt-90) cc_final: 0.6950 (mtt180) REVERT: C 807 ASP cc_start: 0.8303 (m-30) cc_final: 0.8054 (m-30) REVERT: C 835 LEU cc_start: 0.8900 (tp) cc_final: 0.8561 (tt) REVERT: E 399 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: E 429 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7537 (mm-30) REVERT: E 535 GLU cc_start: 0.8221 (mm-30) cc_final: 0.8002 (mp0) REVERT: E 564 GLN cc_start: 0.8668 (mm110) cc_final: 0.8387 (mp10) REVERT: E 879 ARG cc_start: 0.7630 (mmp-170) cc_final: 0.6704 (mtt90) outliers start: 28 outliers final: 18 residues processed: 201 average time/residue: 1.1963 time to fit residues: 257.4766 Evaluate side-chains 207 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 759 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9158 Z= 0.319 Angle : 0.561 6.211 12462 Z= 0.277 Chirality : 0.043 0.186 1504 Planarity : 0.005 0.060 1494 Dihedral : 8.435 86.970 1467 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.47 % Allowed : 15.58 % Favored : 80.95 % 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: 1.76 (0.25), residues: 1102 helix: 1.69 (0.18), residues: 744 sheet: None (None), residues: 0 loop : 0.18 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 492 HIS 0.002 0.001 HIS E 651 PHE 0.018 0.002 PHE C 511 TYR 0.016 0.002 TYR C 824 ARG 0.005 0.001 ARG C 603 *********************** 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 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: C 426 LEU cc_start: 0.8885 (mt) cc_final: 0.8660 (mm) REVERT: C 472 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 473 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: C 646 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.5715 (ppp80) REVERT: C 656 ARG cc_start: 0.7917 (mmt-90) cc_final: 0.7000 (mtt180) REVERT: C 752 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.6353 (mt0) REVERT: C 807 ASP cc_start: 0.8384 (m-30) cc_final: 0.8128 (m-30) REVERT: E 399 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: E 429 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7495 (mm-30) REVERT: E 542 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8300 (tptp) REVERT: E 879 ARG cc_start: 0.7682 (mmp-170) cc_final: 0.6735 (mtt90) outliers start: 33 outliers final: 16 residues processed: 202 average time/residue: 1.1600 time to fit residues: 250.2531 Evaluate side-chains 201 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 542 LYS Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 807 ASP Chi-restraints excluded: chain E residue 844 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.0060 chunk 9 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 564 GLN E 759 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9158 Z= 0.155 Angle : 0.477 5.913 12462 Z= 0.238 Chirality : 0.039 0.176 1504 Planarity : 0.005 0.058 1494 Dihedral : 8.150 82.956 1467 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.42 % Allowed : 16.74 % Favored : 80.84 % 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: 2.04 (0.25), residues: 1102 helix: 1.92 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.25 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 PHE 0.016 0.001 PHE C 511 TYR 0.019 0.001 TYR C 824 ARG 0.008 0.000 ARG E 827 *********************** 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 204 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7555 (mtt180) REVERT: C 426 LEU cc_start: 0.8861 (mt) cc_final: 0.8644 (mm) REVERT: C 472 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8269 (mm-30) REVERT: C 473 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: C 646 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.5961 (ppp80) REVERT: C 656 ARG cc_start: 0.7880 (mmt-90) cc_final: 0.6963 (mtt180) REVERT: C 807 ASP cc_start: 0.8316 (m-30) cc_final: 0.8095 (m-30) REVERT: C 835 LEU cc_start: 0.8935 (tp) cc_final: 0.8580 (tt) REVERT: E 399 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: E 429 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7374 (mm-30) REVERT: E 535 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7990 (mp0) REVERT: E 807 ASP cc_start: 0.8352 (m-30) cc_final: 0.8123 (m-30) REVERT: E 879 ARG cc_start: 0.7647 (mmp-170) cc_final: 0.6647 (mtt90) outliers start: 23 outliers final: 13 residues processed: 193 average time/residue: 1.1588 time to fit residues: 239.6161 Evaluate side-chains 196 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 759 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9158 Z= 0.172 Angle : 0.480 5.876 12462 Z= 0.240 Chirality : 0.040 0.167 1504 Planarity : 0.005 0.059 1494 Dihedral : 8.037 82.782 1467 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.00 % Allowed : 17.68 % Favored : 80.32 % 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: 1.95 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.26 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 PHE 0.017 0.001 PHE C 511 TYR 0.018 0.001 TYR C 824 ARG 0.004 0.000 ARG C 603 *********************** 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 196 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7520 (mtt180) REVERT: C 426 LEU cc_start: 0.8858 (mt) cc_final: 0.8653 (mm) REVERT: C 472 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8264 (mm-30) REVERT: C 473 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7458 (mt-10) REVERT: C 646 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.5919 (ppp80) REVERT: C 656 ARG cc_start: 0.7884 (mmt-90) cc_final: 0.6964 (mtt180) REVERT: C 752 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6424 (mt0) REVERT: C 807 ASP cc_start: 0.8320 (m-30) cc_final: 0.8098 (m-30) REVERT: C 835 LEU cc_start: 0.8931 (tp) cc_final: 0.8568 (tt) REVERT: E 399 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: E 429 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7354 (mm-30) REVERT: E 535 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7982 (mp0) REVERT: E 879 ARG cc_start: 0.7641 (mmp-170) cc_final: 0.6683 (mtt90) outliers start: 19 outliers final: 16 residues processed: 187 average time/residue: 1.1430 time to fit residues: 228.6464 Evaluate side-chains 198 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.0060 chunk 9 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 759 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9158 Z= 0.199 Angle : 0.491 5.904 12462 Z= 0.245 Chirality : 0.040 0.168 1504 Planarity : 0.005 0.059 1494 Dihedral : 7.897 82.600 1464 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.42 % Allowed : 17.26 % Favored : 80.32 % 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: 2.05 (0.25), residues: 1102 helix: 1.91 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.26 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 PHE 0.018 0.001 PHE C 511 TYR 0.018 0.001 TYR C 824 ARG 0.005 0.000 ARG C 603 ********************** 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 202 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: C 426 LEU cc_start: 0.8864 (mt) cc_final: 0.8655 (mm) REVERT: C 472 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8259 (mm-30) REVERT: C 646 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.5828 (ppp80) REVERT: C 656 ARG cc_start: 0.7890 (mmt-90) cc_final: 0.6975 (mtt180) REVERT: C 752 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6437 (mt0) REVERT: C 807 ASP cc_start: 0.8324 (m-30) cc_final: 0.8091 (m-30) REVERT: C 835 LEU cc_start: 0.8945 (tp) cc_final: 0.8592 (tt) REVERT: E 399 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: E 535 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7971 (mp0) REVERT: E 542 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8202 (tttp) REVERT: E 879 ARG cc_start: 0.7648 (mmp-170) cc_final: 0.6683 (mtt90) outliers start: 23 outliers final: 16 residues processed: 190 average time/residue: 1.1705 time to fit residues: 237.6853 Evaluate side-chains 197 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 542 LYS Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 864 ILE 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: 0.8980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 759 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.131898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.109685 restraints weight = 10367.762| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.44 r_work: 0.2973 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9158 Z= 0.137 Angle : 0.459 5.797 12462 Z= 0.231 Chirality : 0.039 0.161 1504 Planarity : 0.005 0.059 1494 Dihedral : 7.729 80.724 1464 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.00 % Allowed : 17.79 % Favored : 80.21 % 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: 2.17 (0.25), residues: 1102 helix: 2.04 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.20 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 PHE 0.019 0.001 PHE C 511 TYR 0.018 0.001 TYR C 824 ARG 0.005 0.000 ARG C 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6156.38 seconds wall clock time: 109 minutes 5.49 seconds (6545.49 seconds total)