Starting phenix.real_space_refine on Fri Jul 3 05:17:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ecp_47924/07_2026/9ecp_47924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ecp_47924/07_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_47924/07_2026/9ecp_47924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ecp_47924/07_2026/9ecp_47924.map" model { file = "/net/cci-nas-00/data/ceres_data/9ecp_47924/07_2026/9ecp_47924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ecp_47924/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.08, per 1000 atoms: 0.25 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: 0.86 Conformation dependent library (CDL) restraints added in 558.1 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: 1.85 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: 2.32 Time building geometry restraints manager: 1.21 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: 17615 1.97 - 3.93: 1033 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: 18.220 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: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- 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 : 0.926 9.825 18709 Z= 0.746 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 0.92648 / 0.75 (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 : 0.324 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.9343 time to fit residues: 124.0252 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 : 0.310 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.212834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.166944 restraints weight = 43479.792| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 0.99 r_work: 0.3395 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 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 = 0.3305 r_free = 0.3305 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: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12894 Z= 0.158 Angle : 0.678 7.421 18709 Z= 0.395 Chirality : 0.047 0.228 2128 Planarity : 0.005 0.039 1385 Dihedral : 30.356 83.816 4053 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.95 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 0.013 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.16 (12894) covalent geometry : angle 0.67797 / 0.39 (18709) hydrogen bonds : bond 0.06219 / 4.23 ( 799) hydrogen bonds : angle 3.14384 / 2.26 ( 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 : 0.322 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.0169 time to fit residues: 143.4824 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 : 0.226 ------------------------------------------------------------------------------- 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: 0.2980 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 76 optimal weight: 30.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.206596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.159579 restraints weight = 37555.552| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.00 r_work: 0.3327 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12894 Z= 0.238 Angle : 0.829 9.189 18709 Z= 0.457 Chirality : 0.054 0.249 2128 Planarity : 0.007 0.081 1385 Dihedral : 30.598 79.686 4053 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.15 % Allowed : 9.23 % Favored : 90.62 % 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: 2.77 (0.28), residues: 787 helix: 2.43 (0.20), residues: 578 sheet: None (None), residues: 0 loop : 0.15 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 116 TYR 0.020 0.003 TYR F 51 PHE 0.010 0.002 PHE C 25 HIS 0.008 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.24 (12894) covalent geometry : angle 0.82878 / 0.46 (18709) hydrogen bonds : bond 0.08261 / 5.57 ( 799) hydrogen bonds : angle 3.61380 / 2.61 ( 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 134 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.307 Fit side-chains REVERT: D 72 GLU cc_start: 0.8589 (pp20) cc_final: 0.8358 (pp20) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.9334 time to fit residues: 130.7602 Evaluate side-chains 132 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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: 0.6980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 30.0000 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 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 = 0.4326 r_free = 0.4326 target = 0.209931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.164065 restraints weight = 41195.835| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.02 r_work: 0.3357 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0921 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= 0.162 Angle : 0.717 7.714 18709 Z= 0.406 Chirality : 0.049 0.240 2128 Planarity : 0.004 0.032 1385 Dihedral : 30.695 81.784 4053 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.15 % Allowed : 9.08 % Favored : 90.77 % 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: 2.85 (0.28), residues: 787 helix: 2.55 (0.20), residues: 582 sheet: None (None), residues: 0 loop : -0.08 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 67 TYR 0.014 0.002 TYR E 54 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.16 (12894) covalent geometry : angle 0.71675 / 0.41 (18709) hydrogen bonds : bond 0.06315 / 4.29 ( 799) hydrogen bonds : angle 3.27849 / 2.35 ( 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 136 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.327 Fit side-chains REVERT: D 72 GLU cc_start: 0.8603 (pp20) cc_final: 0.8328 (pp20) REVERT: H 72 GLU cc_start: 0.8603 (pp20) cc_final: 0.8351 (pp20) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 1.0581 time to fit residues: 149.1004 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 : 0.377 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 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: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.206323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.159212 restraints weight = 38196.684| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.01 r_work: 0.3300 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12894 Z= 0.246 Angle : 0.831 9.302 18709 Z= 0.457 Chirality : 0.055 0.252 2128 Planarity : 0.007 0.078 1385 Dihedral : 30.681 80.490 4053 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.15 % Allowed : 9.08 % Favored : 90.77 % 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: 2.63 (0.27), residues: 787 helix: 2.35 (0.20), residues: 578 sheet: None (None), residues: 0 loop : 0.04 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 116 TYR 0.021 0.003 TYR F 51 PHE 0.010 0.002 PHE E 84 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.25 (12894) covalent geometry : angle 0.83121 / 0.46 (18709) hydrogen bonds : bond 0.08247 / 5.56 ( 799) hydrogen bonds : angle 3.62821 / 2.62 ( 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: 1 poor density : 132 time to evaluate : 0.255 Fit side-chains REVERT: B 93 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8155 (mt0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 1.0254 time to fit residues: 141.3171 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.7980 chunk 87 optimal weight: 30.0000 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.208671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.161895 restraints weight = 44982.077| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.04 r_work: 0.3350 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 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: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12894 Z= 0.170 Angle : 0.734 7.588 18709 Z= 0.413 Chirality : 0.050 0.242 2128 Planarity : 0.005 0.041 1385 Dihedral : 30.756 81.877 4053 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.15 % Allowed : 10.00 % Favored : 89.85 % 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: 2.84 (0.28), residues: 787 helix: 2.56 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -0.11 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 20 TYR 0.015 0.002 TYR F 51 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.17 (12894) covalent geometry : angle 0.73427 / 0.41 (18709) hydrogen bonds : bond 0.06754 / 4.58 ( 799) hydrogen bonds : angle 3.36342 / 2.42 ( 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 136 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.326 Fit side-chains REVERT: B 93 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: D 72 GLU cc_start: 0.8592 (pp20) cc_final: 0.8347 (pp20) REVERT: H 72 GLU cc_start: 0.8620 (pp20) cc_final: 0.8400 (pp20) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.9206 time to fit residues: 130.0428 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.208909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.161980 restraints weight = 43528.843| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 0.98 r_work: 0.3357 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 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 = 0.3251 r_free = 0.3251 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: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12894 Z= 0.167 Angle : 0.724 8.823 18709 Z= 0.408 Chirality : 0.049 0.237 2128 Planarity : 0.005 0.037 1385 Dihedral : 30.741 82.302 4053 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 2.99 (0.28), residues: 787 helix: 2.66 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -0.04 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.016 0.002 TYR F 51 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.17 (12894) covalent geometry : angle 0.72392 / 0.41 (18709) hydrogen bonds : bond 0.06676 / 4.51 ( 799) hydrogen bonds : angle 3.31516 / 2.39 ( 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 137 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.198 Fit side-chains REVERT: B 93 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: D 72 GLU cc_start: 0.8603 (pp20) cc_final: 0.8330 (pp20) REVERT: H 72 GLU cc_start: 0.8637 (pp20) cc_final: 0.8399 (pp20) outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 1.0291 time to fit residues: 145.1512 Evaluate side-chains 136 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN 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: 1.9990 chunk 9 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.208081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.161031 restraints weight = 44434.072| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.00 r_work: 0.3342 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 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 = 0.3234 r_free = 0.3234 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: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12894 Z= 0.196 Angle : 0.746 7.775 18709 Z= 0.418 Chirality : 0.050 0.236 2128 Planarity : 0.006 0.054 1385 Dihedral : 30.709 81.796 4053 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.15 % Allowed : 9.08 % Favored : 90.77 % 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: 2.89 (0.28), residues: 787 helix: 2.57 (0.20), residues: 578 sheet: None (None), residues: 0 loop : 0.03 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 116 TYR 0.018 0.002 TYR F 51 PHE 0.009 0.002 PHE E 67 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.20 (12894) covalent geometry : angle 0.74598 / 0.42 (18709) hydrogen bonds : bond 0.07139 / 4.81 ( 799) hydrogen bonds : angle 3.42516 / 2.47 ( 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 134 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.324 Fit side-chains REVERT: B 93 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: D 72 GLU cc_start: 0.8603 (pp20) cc_final: 0.8332 (pp20) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.9911 time to fit residues: 137.6673 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.209453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.162973 restraints weight = 40640.549| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 0.95 r_work: 0.3350 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.116 | | 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) = 0.116 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12894 Z= 0.156 Angle : 0.704 7.117 18709 Z= 0.401 Chirality : 0.048 0.229 2128 Planarity : 0.005 0.035 1385 Dihedral : 30.729 82.546 4053 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 2.99 (0.28), residues: 787 helix: 2.65 (0.20), residues: 582 sheet: None (None), residues: 0 loop : -0.01 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 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 0.00239 / 0.16 (12894) covalent geometry : angle 0.70353 / 0.40 (18709) hydrogen bonds : bond 0.06531 / 4.41 ( 799) hydrogen bonds : angle 3.26864 / 2.35 ( 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 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.351 Fit side-chains REVERT: B 93 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8109 (mt0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 1.1143 time to fit residues: 153.5595 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN 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: 1.9990 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 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: 1.9990 chunk 75 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.208467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.161915 restraints weight = 37740.443| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 0.96 r_work: 0.3327 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 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 = 0.3238 r_free = 0.3238 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: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12894 Z= 0.190 Angle : 0.737 7.551 18709 Z= 0.414 Chirality : 0.050 0.232 2128 Planarity : 0.005 0.050 1385 Dihedral : 30.713 81.879 4053 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.59 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: 2.95 (0.28), residues: 787 helix: 2.62 (0.20), residues: 578 sheet: None (None), residues: 0 loop : 0.05 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.018 0.002 TYR F 51 PHE 0.009 0.002 PHE E 67 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.19 (12894) covalent geometry : angle 0.73717 / 0.41 (18709) hydrogen bonds : bond 0.06965 / 4.69 ( 799) hydrogen bonds : angle 3.38043 / 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 134 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.369 Fit side-chains REVERT: B 93 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: D 72 GLU cc_start: 0.8600 (pp20) cc_final: 0.8379 (pp20) REVERT: H 72 GLU cc_start: 0.8604 (pp20) cc_final: 0.8398 (pp20) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 1.1197 time to fit residues: 155.4041 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 : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.209705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.163400 restraints weight = 44584.355| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.01 r_work: 0.3363 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 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 = 0.3248 r_free = 0.3248 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: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12894 Z= 0.155 Angle : 0.695 7.053 18709 Z= 0.398 Chirality : 0.048 0.226 2128 Planarity : 0.004 0.034 1385 Dihedral : 30.724 82.583 4053 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 3.01 (0.28), residues: 787 helix: 2.66 (0.20), residues: 582 sheet: None (None), residues: 0 loop : 0.00 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 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 0.00235 / 0.16 (12894) covalent geometry : angle 0.69454 / 0.40 (18709) hydrogen bonds : bond 0.06437 / 4.35 ( 799) hydrogen bonds : angle 3.25449 / 2.34 ( 2003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7048.52 seconds wall clock time: 120 minutes 0.47 seconds (7200.47 seconds total)