Starting phenix.real_space_refine (version: dev) on Sat Feb 18 22:53:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2023/7v19_26954_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.109 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 Process input model Symmetric amino acids flipped Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 596": "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 "E TYR 553": "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 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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 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: 5.50, per 1000 atoms: 0.62 Number of scatterers: 8936 At special positions: 0 Unit cell: (146.495, 91.3, 80.925, 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: 3.42 Conformation dependent library (CDL) restraints added in 1.4 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 66.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 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: 5.051A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 430 removed outlier: 3.758A 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: 3.596A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.599A pdb=" N LEU C 512 " --> pdb=" O GLY C 509 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 513 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 546 removed outlier: 3.533A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.765A 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: 3.788A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA C 668 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 5.200A 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 704 through 718 removed outlier: 3.533A 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: 4.441A 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: 4.184A 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 393 Proline residue: E 391 - end of helix Processing helix chain 'E' and resid 395 through 400 removed outlier: 5.357A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 430 removed outlier: 3.680A 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: 3.789A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.508A pdb=" N LEU E 512 " --> pdb=" O GLY E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 546 Processing helix chain 'E' and resid 570 through 593 removed outlier: 3.728A 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: 3.746A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA E 668 " --> pdb=" O MET E 664 " (cutoff:3.500A) removed outlier: 5.504A 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 718 removed outlier: 3.772A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (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: 4.193A pdb=" N ARG E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 800 removed outlier: 3.954A pdb=" N LEU E 800 " --> pdb=" O GLY E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 813 removed outlier: 3.502A pdb=" N LEU E 812 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 4.158A 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 874 through 876 No H-bonds generated for 'chain 'E' and resid 874 through 876' 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: 4.979A 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 741 490 hydrogen bonds defined for protein. 1410 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: 2.48 Time building geometry restraints manager: 3.70 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: 2442 1.43 - 1.56: 5328 1.56 - 1.68: 8 1.68 - 1.81: 70 Bond restraints: 9158 Sorted by residual: bond pdb=" C VAL E 867 " pdb=" N PRO E 868 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.09e+00 bond pdb=" CA VAL E 634 " pdb=" CB VAL E 634 " ideal model delta sigma weight residual 1.546 1.538 0.009 8.80e-03 1.29e+04 9.76e-01 bond pdb=" C VAL C 867 " pdb=" N PRO C 868 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 9.12e-01 bond pdb=" C VAL E 610 " pdb=" N PRO E 611 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.36e-02 5.41e+03 7.45e-01 bond pdb=" CA VAL C 822 " pdb=" CB VAL C 822 " ideal model delta sigma weight residual 1.537 1.548 -0.011 1.29e-02 6.01e+03 7.40e-01 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.73: 270 105.73 - 112.79: 5031 112.79 - 119.84: 2834 119.84 - 126.90: 4210 126.90 - 133.95: 117 Bond angle restraints: 12462 Sorted by residual: angle pdb=" C ARG E 389 " pdb=" N TYR E 390 " pdb=" CA TYR E 390 " ideal model delta sigma weight residual 120.06 123.35 -3.29 1.19e+00 7.06e-01 7.63e+00 angle pdb=" C ARG C 389 " pdb=" N TYR C 390 " pdb=" CA TYR C 390 " ideal model delta sigma weight residual 120.06 123.03 -2.97 1.19e+00 7.06e-01 6.21e+00 angle pdb=" C THR E 866 " pdb=" N VAL E 867 " pdb=" CA VAL E 867 " ideal model delta sigma weight residual 120.33 122.22 -1.89 8.00e-01 1.56e+00 5.61e+00 angle pdb=" N ASN E 569 " pdb=" CA ASN E 569 " pdb=" CB ASN E 569 " ideal model delta sigma weight residual 113.65 110.40 3.25 1.47e+00 4.63e-01 4.88e+00 angle pdb=" C TYR E 596 " pdb=" N PHE E 597 " pdb=" CA PHE E 597 " ideal model delta sigma weight residual 121.80 126.59 -4.79 2.44e+00 1.68e-01 3.85e+00 ... (remaining 12457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.38: 5125 20.38 - 40.77: 165 40.77 - 61.15: 36 61.15 - 81.54: 3 81.54 - 101.92: 9 Dihedral angle restraints: 5338 sinusoidal: 2136 harmonic: 3202 Sorted by residual: 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 50.00 -51.92 101.92 1 2.00e+01 2.50e-03 2.90e+01 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 50.00 -51.33 101.33 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" C1 NAG A 2 " pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " ideal model delta sinusoidal sigma weight residual -50.00 37.67 -87.67 1 2.00e+01 2.50e-03 2.30e+01 ... (remaining 5335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 895 0.025 - 0.050: 334 0.050 - 0.075: 174 0.075 - 0.101: 61 0.101 - 0.126: 40 Chirality restraints: 1504 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 6.21e-01 chirality pdb=" CA ILE E 516 " pdb=" N ILE E 516 " pdb=" C ILE E 516 " pdb=" CB ILE E 516 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL E 828 " pdb=" N VAL E 828 " pdb=" C VAL E 828 " pdb=" CB VAL E 828 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 1501 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 390 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+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 TYR E 390 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO E 391 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 466 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO C 467 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 467 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 467 " -0.025 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 350 2.73 - 3.27: 9212 3.27 - 3.81: 15154 3.81 - 4.36: 18328 4.36 - 4.90: 31139 Nonbonded interactions: 74183 Sorted by model distance: nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.186 2.440 nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.228 2.440 nonbonded pdb=" O VAL C 850 " pdb=" OG1 THR C 853 " model vdw 2.283 2.440 nonbonded pdb=" O LEU C 427 " pdb=" OG1 THR C 431 " model vdw 2.287 2.440 nonbonded pdb=" O LEU E 427 " pdb=" OG1 THR E 431 " model vdw 2.324 2.440 ... (remaining 74178 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 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. 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: 4.930 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: 16.070 Check model and map are aligned: 0.130 Process input model: 25.750 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.002 0.026 9158 Z= 0.136 Angle : 0.500 5.695 12462 Z= 0.273 Chirality : 0.039 0.126 1504 Planarity : 0.005 0.062 1494 Dihedral : 11.700 101.922 3274 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 1.16 % 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: 1.59 (0.24), residues: 1102 helix: 1.56 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.11 (0.31), residues: 362 *********************** 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 199 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 197 average time/residue: 0.2303 time to fit residues: 61.1651 Evaluate side-chains 148 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1050 time to fit residues: 1.6272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS D 82 GLN C 377 GLN C 404 GLN C 630 GLN C 651 HIS E 377 GLN E 434 GLN E 457 GLN E 630 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN E 804 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 9158 Z= 0.349 Angle : 0.594 5.855 12462 Z= 0.295 Chirality : 0.044 0.186 1504 Planarity : 0.005 0.058 1494 Dihedral : 9.885 105.706 1264 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.53 % 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: 1.51 (0.24), residues: 1102 helix: 1.52 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 0.09 (0.30), residues: 372 *********************** 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 176 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.112 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 168 average time/residue: 0.2043 time to fit residues: 48.4523 Evaluate side-chains 148 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0844 time to fit residues: 3.3665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 GLN C 651 HIS C 683 GLN C 819 HIS C 884 GLN E 569 ASN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 819 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 9158 Z= 0.142 Angle : 0.467 5.510 12462 Z= 0.232 Chirality : 0.039 0.177 1504 Planarity : 0.004 0.054 1494 Dihedral : 9.562 103.783 1264 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 0.84 % 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: 1.95 (0.25), residues: 1102 helix: 1.84 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.33 (0.31), residues: 374 *********************** 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 150 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.045 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 146 average time/residue: 0.1980 time to fit residues: 41.9567 Evaluate side-chains 135 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1223 time to fit residues: 1.6265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9158 Z= 0.201 Angle : 0.490 5.751 12462 Z= 0.243 Chirality : 0.041 0.181 1504 Planarity : 0.004 0.052 1494 Dihedral : 9.519 104.675 1264 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.95 % 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: 1.89 (0.25), residues: 1102 helix: 1.81 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 0.25 (0.31), residues: 372 *********************** 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 147 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 0.979 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 143 average time/residue: 0.2017 time to fit residues: 41.0933 Evaluate side-chains 143 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0843 time to fit residues: 2.0521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9158 Z= 0.151 Angle : 0.467 5.565 12462 Z= 0.232 Chirality : 0.039 0.185 1504 Planarity : 0.004 0.053 1494 Dihedral : 9.413 104.163 1264 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.05 % 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: 1.98 (0.25), residues: 1102 helix: 1.90 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.24 (0.31), residues: 374 *********************** 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 157 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 0.990 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 151 average time/residue: 0.1955 time to fit residues: 42.8130 Evaluate side-chains 149 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1189 time to fit residues: 2.9966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9158 Z= 0.161 Angle : 0.470 5.801 12462 Z= 0.233 Chirality : 0.039 0.182 1504 Planarity : 0.004 0.052 1494 Dihedral : 9.364 104.250 1264 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.74 % 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: 2.01 (0.25), residues: 1102 helix: 1.92 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.27 (0.31), residues: 374 *********************** 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 150 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 0.989 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 146 average time/residue: 0.1999 time to fit residues: 41.7718 Evaluate side-chains 147 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0846 time to fit residues: 2.0436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 0.0670 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9158 Z= 0.136 Angle : 0.460 5.666 12462 Z= 0.227 Chirality : 0.039 0.193 1504 Planarity : 0.004 0.052 1494 Dihedral : 9.275 104.004 1264 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 0.42 % 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: 2.14 (0.25), residues: 1102 helix: 2.02 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.32 (0.32), residues: 374 *********************** 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 145 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.009 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 143 average time/residue: 0.2035 time to fit residues: 41.6784 Evaluate side-chains 145 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0968 time to fit residues: 1.9242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 9158 Z= 0.281 Angle : 0.541 8.847 12462 Z= 0.267 Chirality : 0.042 0.189 1504 Planarity : 0.005 0.051 1494 Dihedral : 9.489 105.097 1264 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.63 % 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: 1.81 (0.25), residues: 1102 helix: 1.76 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.20 (0.31), residues: 374 *********************** 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 147 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 144 average time/residue: 0.2266 time to fit residues: 45.6468 Evaluate side-chains 139 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0845 time to fit residues: 1.7680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2484 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= 0.221 Angle : 0.511 8.562 12462 Z= 0.252 Chirality : 0.040 0.194 1504 Planarity : 0.004 0.052 1494 Dihedral : 9.441 104.423 1264 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.42 % 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: 1.80 (0.25), residues: 1102 helix: 1.83 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 0.08 (0.31), residues: 386 *********************** 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 139 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.002 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 137 average time/residue: 0.1934 time to fit residues: 38.1837 Evaluate side-chains 133 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1144 time to fit residues: 1.8370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9158 Z= 0.171 Angle : 0.491 8.562 12462 Z= 0.242 Chirality : 0.040 0.201 1504 Planarity : 0.004 0.052 1494 Dihedral : 9.331 104.173 1264 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.11 % 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: 2.00 (0.25), residues: 1102 helix: 1.98 (0.19), residues: 712 sheet: None (None), residues: 0 loop : 0.19 (0.31), residues: 390 ********************** 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 141 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 0.925 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.1965 time to fit residues: 40.1371 Evaluate side-chains 138 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0830 time to fit residues: 1.4834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 0.0050 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 76 optimal weight: 0.0270 chunk 4 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 overall best weight: 0.3452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.161635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.137861 restraints weight = 10157.947| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.56 r_work: 0.3336 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 9158 Z= 0.118 Angle : 0.468 8.251 12462 Z= 0.228 Chirality : 0.039 0.240 1504 Planarity : 0.004 0.053 1494 Dihedral : 9.152 103.589 1264 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 0.21 % 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: 2.13 (0.25), residues: 1102 helix: 2.05 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.22 (0.32), residues: 374 =============================================================================== Job complete usr+sys time: 2867.26 seconds wall clock time: 52 minutes 32.26 seconds (3152.26 seconds total)