Starting phenix.real_space_refine on Wed Aug 5 23:28:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ecp_47924/08_2026/9ecp_47924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ecp_47924/08_2026/9ecp_47924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ecp_47924/08_2026/9ecp_47924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ecp_47924/08_2026/9ecp_47924.map" model { file = "/net/cci-nas-00/data/ceres_data/9ecp_47924/08_2026/9ecp_47924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ecp_47924/08_2026/9ecp_47924.cif" } resolution = 1.91 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 288 5.49 5 S 14 5.16 5 C 6662 2.51 5 N 2271 2.21 5 O 3004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12239 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Conformer: "B" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} bond proxies already assigned to first conformer: 788 Chain: "B" Number of atoms: 660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 639 Chain: "C" Number of atoms: 842 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 834 Chain: "D" Number of atoms: 757 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 698 Chain: "E" Number of atoms: 804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Conformer: "B" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} bond proxies already assigned to first conformer: 788 Chain: "F" Number of atoms: 664 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 635 Chain: "G" Number of atoms: 842 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 834 Chain: "H" Number of atoms: 757 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 698 Chain: "I" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AARG A 83 " occ=0.37 ... (20 atoms not shown) pdb=" NH2BARG A 83 " occ=0.63 residue: pdb=" N ASER C 18 " occ=0.87 ... (10 atoms not shown) pdb=" OG BSER C 18 " occ=0.13 residue: pdb=" N ASER D 39 " occ=0.36 ... (10 atoms not shown) pdb=" OG BSER D 39 " occ=0.64 residue: pdb=" N AASN D 64 " occ=0.43 ... (14 atoms not shown) pdb=" ND2BASN D 64 " occ=0.57 residue: pdb=" N ASER D 65 " occ=0.43 ... (10 atoms not shown) pdb=" OG BSER D 65 " occ=0.57 residue: pdb=" N ASER D 92 " occ=0.49 ... (10 atoms not shown) pdb=" OG BSER D 92 " occ=0.51 residue: pdb=" N AARG E 83 " occ=0.24 ... (20 atoms not shown) pdb=" NH2BARG E 83 " occ=0.76 residue: pdb=" N ASER F 47 " occ=0.74 ... (10 atoms not shown) pdb=" OG BSER F 47 " occ=0.26 residue: pdb=" N ASER H 39 " occ=0.37 ... (10 atoms not shown) pdb=" OG BSER H 39 " occ=0.63 residue: pdb=" N AASN H 64 " occ=0.30 ... (14 atoms not shown) pdb=" ND2BASN H 64 " occ=0.70 residue: pdb=" N ASER H 65 " occ=0.30 ... (10 atoms not shown) pdb=" OG BSER H 65 " occ=0.70 residue: pdb=" N ASER H 92 " occ=0.55 ... (10 atoms not shown) pdb=" OG BSER H 92 " occ=0.45 Time building chain proxies: 3.87, per 1000 atoms: 0.32 Number of scatterers: 12239 At special positions: 0 Unit cell: (122.4, 74.97, 115.26, 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 14 16.00 P 288 15.00 O 3004 8.00 N 2271 7.00 C 6662 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 723.9 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.7% alpha, 3.1% beta 144 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.645A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.639A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.305A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 44 through 56 removed outlier: 4.027A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.506A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.878A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.687A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.314A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.885A pdb=" N AARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.026A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.912A pdb=" N AARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.046A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 429 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2211 1.33 - 1.45: 4349 1.45 - 1.57: 5731 1.57 - 1.70: 579 1.70 - 1.82: 24 Bond restraints: 12894 Sorted by residual: bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA I 6 " pdb=" O3' DA I 6 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" C1' DT I 69 " pdb=" N1 DT I 69 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.14e+01 bond pdb=" C3' DT J -39 " pdb=" C2' DT J -39 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C1' DC I -4 " pdb=" N1 DC I -4 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.12e+01 ... (remaining 12889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17593 1.97 - 3.93: 1055 3.93 - 5.90: 37 5.90 - 7.86: 18 7.86 - 9.83: 6 Bond angle restraints: 18709 Sorted by residual: angle pdb=" N3 DT I 69 " pdb=" C4 DT I 69 " pdb=" O4 DT I 69 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" CA GLU G 91 " pdb=" CB GLU G 91 " pdb=" CG GLU G 91 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.99e+01 angle pdb=" N3 DT J -59 " pdb=" C4 DT J -59 " pdb=" O4 DT J -59 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" CA GLU C 91 " pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " ideal model delta sigma weight residual 114.10 122.96 -8.86 2.00e+00 2.50e-01 1.96e+01 ... (remaining 18704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4559 17.95 - 35.90: 1079 35.90 - 53.85: 1142 53.85 - 71.79: 241 71.79 - 89.74: 16 Dihedral angle restraints: 7037 sinusoidal: 4744 harmonic: 2293 Sorted by residual: dihedral pdb=" CA LYS C 15 " pdb=" C LYS C 15 " pdb=" N SER C 16 " pdb=" CA SER C 16 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP G 90 " pdb=" CB ASP G 90 " pdb=" CG ASP G 90 " pdb=" OD1 ASP G 90 " ideal model delta sinusoidal sigma weight residual -30.00 -86.67 56.67 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 7034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1204 0.038 - 0.077: 645 0.077 - 0.115: 228 0.115 - 0.153: 45 0.153 - 0.192: 6 Chirality restraints: 2128 Sorted by residual: chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" C4' DA I -35 " pdb=" C5' DA I -35 " pdb=" O4' DA I -35 " pdb=" C3' DA I -35 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" C4' DA I 47 " pdb=" C5' DA I 47 " pdb=" O4' DA I 47 " pdb=" C3' DA I 47 " both_signs ideal model delta sigma weight residual False -2.53 -2.36 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 2125 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " -0.035 2.00e-02 2.50e+03 1.53e-02 6.43e+00 pdb=" N9 DA I 17 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.034 2.00e-02 2.50e+03 1.48e-02 6.02e+00 pdb=" N9 DA I 47 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO G 80 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1383 2.76 - 3.30: 10388 3.30 - 3.83: 24616 3.83 - 4.37: 29818 4.37 - 4.90: 41664 Nonbonded interactions: 107869 Sorted by model distance: nonbonded pdb=" O HOH E 201 " pdb=" O HOH E 203 " model vdw 2.229 3.040 nonbonded pdb=" NZ LYS A 56 " pdb=" O HOH A 201 " model vdw 2.317 3.120 nonbonded pdb=" NZ LYS E 56 " pdb=" O HOH E 201 " model vdw 2.370 3.120 nonbonded pdb=" OG1 THR H 91 " pdb=" OE1 GLU H 94 " model vdw 2.371 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 69 " model vdw 2.378 3.040 ... (remaining 107864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 82 or resid 85 through 133)) selection = (chain 'E' and (resid 38 through 82 or resid 85 through 133)) } ncs_group { reference = (chain 'B' and (resid 21 through 34 or resid 36 through 46 or resid 49 through 1 \ 02)) selection = (chain 'F' and (resid 21 through 34 or resid 36 through 46 or resid 49 through 1 \ 02)) } ncs_group { reference = (chain 'C' and (resid 10 through 17 or resid 20 through 118)) selection = (chain 'G' and (resid 10 through 17 or resid 20 through 118)) } ncs_group { reference = (chain 'D' and (resid 32 through 38 or resid 41 through 63 or resid 67 through 9 \ 1 or resid 94 through 125)) selection = (chain 'H' and (resid 32 through 38 or resid 41 through 63 or resid 67 through 9 \ 1 or resid 94 through 125)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.00 max=1.00 mean=0.99 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: 17.710 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.070 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.007 0.068 12894 Z= 0.588 Angle : 0.936 9.825 18709 Z= 0.756 Chirality : 0.050 0.192 2128 Planarity : 0.006 0.058 1385 Dihedral : 27.628 89.743 5569 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.15 % Allowed : 10.46 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 787 helix: 0.04 (0.18), residues: 572 sheet: None (None), residues: 0 loop : 0.24 (0.36), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 116 TYR 0.014 0.002 TYR C 57 PHE 0.014 0.003 PHE C 25 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.59 (12894) covalent geometry : angle 0.93579 / 0.76 (18709) hydrogen bonds : bond 0.16992 / 11.19 ( 799) hydrogen bonds : angle 4.61506 / 3.30 ( 2003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.1664 time to fit residues: 154.7788 Evaluate side-chains 127 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.213059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.167257 restraints weight = 43527.635| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 0.99 r_work: 0.3401 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12894 Z= 0.153 Angle : 0.693 7.248 18709 Z= 0.398 Chirality : 0.049 0.231 2128 Planarity : 0.005 0.040 1385 Dihedral : 30.296 83.715 4053 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.15 % Allowed : 9.69 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.29), residues: 787 helix: 2.37 (0.21), residues: 582 sheet: None (None), residues: 0 loop : 0.24 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.015 0.001 TYR F 51 PHE 0.014 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.15 (12894) covalent geometry : angle 0.69318 / 0.40 (18709) hydrogen bonds : bond 0.06093 / 4.15 ( 799) hydrogen bonds : angle 3.12127 / 2.25 ( 2003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.0734 time to fit residues: 151.3745 Evaluate side-chains 135 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 31 optimal weight: 0.5980 chunk 76 optimal weight: 30.0000 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.211019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.165068 restraints weight = 39425.970| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 0.96 r_work: 0.3365 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12894 Z= 0.164 Angle : 0.682 7.211 18709 Z= 0.391 Chirality : 0.047 0.222 2128 Planarity : 0.005 0.037 1385 Dihedral : 30.374 82.155 4053 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.31 % Allowed : 9.23 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.29), residues: 787 helix: 2.77 (0.21), residues: 582 sheet: None (None), residues: 0 loop : 0.16 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.015 0.002 TYR F 51 PHE 0.010 0.002 PHE E 67 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.16 (12894) covalent geometry : angle 0.68165 / 0.39 (18709) hydrogen bonds : bond 0.06422 / 4.33 ( 799) hydrogen bonds : angle 3.20662 / 2.31 ( 2003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.343 Fit side-chains REVERT: D 72 GLU cc_start: 0.8575 (pp20) cc_final: 0.8326 (pp20) REVERT: H 72 GLU cc_start: 0.8604 (pp20) cc_final: 0.8350 (pp20) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 1.1404 time to fit residues: 159.6871 Evaluate side-chains 134 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.209709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.163334 restraints weight = 41170.564| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.01 r_work: 0.3343 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12894 Z= 0.175 Angle : 0.712 7.658 18709 Z= 0.401 Chirality : 0.048 0.228 2128 Planarity : 0.005 0.046 1385 Dihedral : 30.487 81.113 4053 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.31 % Allowed : 9.23 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.28), residues: 787 helix: 2.68 (0.20), residues: 582 sheet: None (None), residues: 0 loop : 0.14 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.016 0.002 TYR F 51 PHE 0.009 0.002 PHE E 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.17 (12894) covalent geometry : angle 0.71188 / 0.40 (18709) hydrogen bonds : bond 0.06656 / 4.48 ( 799) hydrogen bonds : angle 3.31167 / 2.39 ( 2003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.352 Fit side-chains REVERT: D 72 GLU cc_start: 0.8645 (pp20) cc_final: 0.8364 (pp20) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 1.1672 time to fit residues: 162.1130 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 94 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.210084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.163872 restraints weight = 39365.962| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 0.98 r_work: 0.3370 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12894 Z= 0.165 Angle : 0.696 7.150 18709 Z= 0.394 Chirality : 0.047 0.226 2128 Planarity : 0.005 0.038 1385 Dihedral : 30.498 81.380 4053 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.15 % Allowed : 9.38 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.28), residues: 787 helix: 2.67 (0.20), residues: 582 sheet: None (None), residues: 0 loop : 0.11 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.015 0.002 TYR F 51 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.17 (12894) covalent geometry : angle 0.69616 / 0.39 (18709) hydrogen bonds : bond 0.06482 / 4.37 ( 799) hydrogen bonds : angle 3.27174 / 2.36 ( 2003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 1.0445 time to fit residues: 145.1621 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.210541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.164045 restraints weight = 45671.052| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.02 r_work: 0.3370 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12894 Z= 0.156 Angle : 0.684 7.612 18709 Z= 0.388 Chirality : 0.047 0.225 2128 Planarity : 0.004 0.032 1385 Dihedral : 30.501 81.658 4053 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.15 % Allowed : 9.54 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.28), residues: 787 helix: 2.71 (0.20), residues: 582 sheet: None (None), residues: 0 loop : 0.10 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.015 0.002 TYR F 51 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.16 (12894) covalent geometry : angle 0.68394 / 0.39 (18709) hydrogen bonds : bond 0.06251 / 4.21 ( 799) hydrogen bonds : angle 3.21827 / 2.32 ( 2003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.285 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 1.0342 time to fit residues: 144.8525 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.210491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.163452 restraints weight = 43737.711| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 0.99 r_work: 0.3370 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12894 Z= 0.159 Angle : 0.679 7.176 18709 Z= 0.386 Chirality : 0.047 0.224 2128 Planarity : 0.004 0.034 1385 Dihedral : 30.500 81.803 4053 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.15 % Allowed : 9.54 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.28), residues: 787 helix: 2.74 (0.20), residues: 582 sheet: None (None), residues: 0 loop : 0.12 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.016 0.002 TYR F 51 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.16 (12894) covalent geometry : angle 0.67915 / 0.39 (18709) hydrogen bonds : bond 0.06170 / 4.16 ( 799) hydrogen bonds : angle 3.20984 / 2.31 ( 2003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.385 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 1.0836 time to fit residues: 150.6612 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 89 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.211053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.164795 restraints weight = 45207.947| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.03 r_work: 0.3373 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 12894 Z= 0.155 Angle : 0.676 8.822 18709 Z= 0.384 Chirality : 0.046 0.223 2128 Planarity : 0.004 0.031 1385 Dihedral : 30.499 81.917 4053 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.15 % Allowed : 9.69 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.28), residues: 787 helix: 2.77 (0.20), residues: 582 sheet: None (None), residues: 0 loop : 0.11 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.015 0.002 TYR F 51 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.16 (12894) covalent geometry : angle 0.67618 / 0.38 (18709) hydrogen bonds : bond 0.06067 / 4.09 ( 799) hydrogen bonds : angle 3.17499 / 2.29 ( 2003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.400 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.9911 time to fit residues: 137.8242 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.208803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.161745 restraints weight = 40228.644| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 0.95 r_work: 0.3356 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12894 Z= 0.190 Angle : 0.739 7.619 18709 Z= 0.412 Chirality : 0.049 0.232 2128 Planarity : 0.006 0.056 1385 Dihedral : 30.536 80.570 4053 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.31 % Allowed : 9.54 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.28), residues: 787 helix: 2.65 (0.20), residues: 578 sheet: None (None), residues: 0 loop : 0.10 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 116 TYR 0.017 0.002 TYR F 51 PHE 0.008 0.002 PHE E 67 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.19 (12894) covalent geometry : angle 0.73901 / 0.41 (18709) hydrogen bonds : bond 0.07010 / 4.71 ( 799) hydrogen bonds : angle 3.38482 / 2.44 ( 2003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.316 Fit side-chains REVERT: D 72 GLU cc_start: 0.8572 (pp20) cc_final: 0.8342 (pp20) REVERT: H 72 GLU cc_start: 0.8592 (pp20) cc_final: 0.8381 (pp20) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 1.1077 time to fit residues: 154.9927 Evaluate side-chains 134 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.208872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.162022 restraints weight = 37952.865| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 0.99 r_work: 0.3355 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12894 Z= 0.190 Angle : 0.745 8.335 18709 Z= 0.414 Chirality : 0.049 0.234 2128 Planarity : 0.005 0.053 1385 Dihedral : 30.573 80.616 4053 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.15 % Allowed : 9.69 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.28), residues: 787 helix: 2.62 (0.20), residues: 578 sheet: None (None), residues: 0 loop : 0.10 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 35 TYR 0.018 0.002 TYR F 51 PHE 0.008 0.002 PHE E 67 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.19 (12894) covalent geometry : angle 0.74501 / 0.41 (18709) hydrogen bonds : bond 0.06931 / 4.66 ( 799) hydrogen bonds : angle 3.37659 / 2.43 ( 2003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.337 Fit side-chains REVERT: D 72 GLU cc_start: 0.8624 (pp20) cc_final: 0.8375 (pp20) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 1.1132 time to fit residues: 154.6098 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 48 GLN G 110 ASN H 48 GLN H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.210140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.163237 restraints weight = 44589.509| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.02 r_work: 0.3365 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12894 Z= 0.160 Angle : 0.707 8.335 18709 Z= 0.397 Chirality : 0.048 0.230 2128 Planarity : 0.005 0.038 1385 Dihedral : 30.586 81.345 4053 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.15 % Allowed : 9.54 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.28), residues: 787 helix: 2.70 (0.20), residues: 582 sheet: None (None), residues: 0 loop : 0.05 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 63 TYR 0.014 0.002 TYR F 51 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.16 (12894) covalent geometry : angle 0.70656 / 0.40 (18709) hydrogen bonds : bond 0.06340 / 4.28 ( 799) hydrogen bonds : angle 3.23148 / 2.33 ( 2003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7633.05 seconds wall clock time: 129 minutes 54.30 seconds (7794.30 seconds total)