Starting phenix.real_space_refine on Wed Feb 4 18:03:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ecp_47924/02_2026/9ecp_47924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ecp_47924/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ecp_47924/02_2026/9ecp_47924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ecp_47924/02_2026/9ecp_47924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ecp_47924/02_2026/9ecp_47924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ecp_47924/02_2026/9ecp_47924.map" } 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-2.0-5952/lib/python3.9/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: 4.28, per 1000 atoms: 0.35 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: 0.94 Conformation dependent library (CDL) restraints added in 609.5 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: 2.62 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: 1.29 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=" CB LYS A 56 " pdb=" CG LYS A 56 " ideal model delta sigma weight residual 1.520 1.588 -0.068 3.00e-02 1.11e+03 5.07e+00 bond pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 4.04e+00 bond pdb=" CB GLU G 91 " pdb=" CG GLU G 91 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.87e+00 bond pdb=" C LYS F 31 " pdb=" N PRO F 32 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.69e+00 bond pdb=" C LYS B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.69e+00 ... (remaining 12889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 18112 1.97 - 3.93: 541 3.93 - 5.90: 32 5.90 - 7.86: 18 7.86 - 9.83: 6 Bond angle restraints: 18709 Sorted by residual: 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=" 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 angle pdb=" CA LYS E 56 " pdb=" CB LYS E 56 " pdb=" CG LYS E 56 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CB LYS A 56 " pdb=" CG LYS A 56 " pdb=" CD LYS A 56 " ideal model delta sigma weight residual 111.30 121.13 -9.83 2.30e+00 1.89e-01 1.82e+01 angle pdb=" CA LYS A 56 " pdb=" CB LYS A 56 " pdb=" CG LYS A 56 " ideal model delta sigma weight residual 114.10 121.18 -7.08 2.00e+00 2.50e-01 1.25e+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 - 0.034: 1343 0.034 - 0.069: 521 0.069 - 0.103: 197 0.103 - 0.137: 51 0.137 - 0.171: 16 Chirality restraints: 2128 Sorted by residual: 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 -0.17 2.00e-01 2.50e+01 7.33e-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 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB ILE H 55 " pdb=" CA ILE H 55 " pdb=" CG1 ILE H 55 " pdb=" CG2 ILE H 55 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.18e-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: 18.710 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.700 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.005 0.068 12894 Z= 0.229 Angle : 0.794 9.825 18709 Z= 0.463 Chirality : 0.044 0.171 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 covalent geometry : bond 0.00475 (12894) covalent geometry : angle 0.79387 (18709) hydrogen bonds : bond 0.16992 ( 799) hydrogen bonds : angle 4.61506 ( 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 : 0.305 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.0712 time to fit residues: 141.6974 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 : 0.326 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4368 r_free = 0.4368 target = 0.214339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.168827 restraints weight = 43609.947| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 0.93 r_work: 0.3417 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12894 Z= 0.160 Angle : 0.576 6.843 18709 Z= 0.351 Chirality : 0.034 0.127 2128 Planarity : 0.004 0.041 1385 Dihedral : 29.961 84.014 4053 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 2.80 (0.29), residues: 787 helix: 2.39 (0.21), residues: 582 sheet: None (None), residues: 0 loop : 0.33 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.014 0.001 TYR F 51 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00317 (12894) covalent geometry : angle 0.57600 (18709) hydrogen bonds : bond 0.05295 ( 799) hydrogen bonds : angle 2.99229 ( 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 : 0.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.0354 time to fit residues: 145.7881 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 : 0.213 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 31 optimal weight: 0.3980 chunk 76 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.208438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.161892 restraints weight = 38809.496| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.01 r_work: 0.3346 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12894 Z= 0.224 Angle : 0.668 7.515 18709 Z= 0.397 Chirality : 0.039 0.169 2128 Planarity : 0.006 0.057 1385 Dihedral : 30.215 81.093 4053 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.31 % Allowed : 8.92 % 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: 3.03 (0.28), residues: 787 helix: 2.63 (0.20), residues: 578 sheet: None (None), residues: 0 loop : 0.22 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 covalent geometry : bond 0.00458 (12894) covalent geometry : angle 0.66766 (18709) hydrogen bonds : bond 0.06889 ( 799) hydrogen bonds : angle 3.34527 ( 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 137 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.275 Fit side-chains REVERT: B 93 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: D 72 GLU cc_start: 0.8576 (pp20) cc_final: 0.8328 (pp20) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 1.0057 time to fit residues: 142.5648 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 : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4319 r_free = 0.4319 target = 0.208927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.162618 restraints weight = 41032.186| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.07 r_work: 0.3324 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 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 = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12894 Z= 0.206 Angle : 0.648 7.459 18709 Z= 0.387 Chirality : 0.038 0.159 2128 Planarity : 0.005 0.045 1385 Dihedral : 30.209 81.632 4053 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.31 % Allowed : 9.38 % 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: 2.62 (0.20), residues: 578 sheet: None (None), residues: 0 loop : 0.13 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.017 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 covalent geometry : bond 0.00418 (12894) covalent geometry : angle 0.64774 (18709) hydrogen bonds : bond 0.06530 ( 799) hydrogen bonds : angle 3.30921 ( 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 135 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.483 Fit side-chains REVERT: B 93 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8137 (mt0) REVERT: H 72 GLU cc_start: 0.8633 (pp20) cc_final: 0.8396 (pp20) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 1.1509 time to fit residues: 160.6379 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 : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4302 r_free = 0.4302 target = 0.207129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.160255 restraints weight = 38856.851| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.02 r_work: 0.3330 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12894 Z= 0.253 Angle : 0.706 7.739 18709 Z= 0.418 Chirality : 0.042 0.181 2128 Planarity : 0.006 0.068 1385 Dihedral : 30.356 81.264 4053 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.77 % Allowed : 8.77 % 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: 2.78 (0.27), residues: 787 helix: 2.46 (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 0.005 0.001 ARG E 116 TYR 0.019 0.002 TYR F 51 PHE 0.009 0.002 PHE E 84 HIS 0.005 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00521 (12894) covalent geometry : angle 0.70636 (18709) hydrogen bonds : bond 0.07388 ( 799) hydrogen bonds : angle 3.46419 ( 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 139 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.333 Fit side-chains REVERT: B 93 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: D 72 GLU cc_start: 0.8606 (pp20) cc_final: 0.8351 (pp20) REVERT: H 72 GLU cc_start: 0.8619 (pp20) cc_final: 0.8361 (pp20) outliers start: 3 outliers final: 0 residues processed: 136 average time/residue: 1.1947 time to fit residues: 169.2997 Evaluate side-chains 137 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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: 10.0000 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.208616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.162246 restraints weight = 44652.455| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.05 r_work: 0.3328 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 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 = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12894 Z= 0.192 Angle : 0.648 8.132 18709 Z= 0.390 Chirality : 0.038 0.141 2128 Planarity : 0.005 0.039 1385 Dihedral : 30.357 82.306 4053 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.46 % Allowed : 8.92 % 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: 2.92 (0.28), residues: 787 helix: 2.61 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -0.03 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 67 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 covalent geometry : bond 0.00386 (12894) covalent geometry : angle 0.64770 (18709) hydrogen bonds : bond 0.06515 ( 799) hydrogen bonds : angle 3.27450 ( 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: 2 poor density : 132 time to evaluate : 0.233 Fit side-chains REVERT: H 72 GLU cc_start: 0.8636 (pp20) cc_final: 0.8384 (pp20) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 1.0237 time to fit residues: 140.9816 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 : 0.313 ------------------------------------------------------------------------------- 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: 0.8980 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.209731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.163382 restraints weight = 44196.933| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 0.98 r_work: 0.3367 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 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 = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12894 Z= 0.181 Angle : 0.628 7.269 18709 Z= 0.379 Chirality : 0.038 0.129 2128 Planarity : 0.004 0.031 1385 Dihedral : 30.327 82.913 4053 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.46 % Allowed : 8.77 % 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: 3.12 (0.28), residues: 787 helix: 2.75 (0.20), residues: 580 sheet: None (None), residues: 0 loop : 0.02 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.016 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 covalent geometry : bond 0.00363 (12894) covalent geometry : angle 0.62796 (18709) hydrogen bonds : bond 0.06044 ( 799) hydrogen bonds : angle 3.18735 ( 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 135 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.282 Fit side-chains REVERT: D 72 GLU cc_start: 0.8585 (pp20) cc_final: 0.8336 (pp20) REVERT: H 72 GLU cc_start: 0.8637 (pp20) cc_final: 0.8382 (pp20) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 1.0853 time to fit residues: 150.4679 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 : 0.205 ------------------------------------------------------------------------------- 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: 4.9990 chunk 9 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4296 r_free = 0.4296 target = 0.206617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.159496 restraints weight = 43665.829| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.07 r_work: 0.3290 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 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 = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12894 Z= 0.265 Angle : 0.723 7.754 18709 Z= 0.426 Chirality : 0.042 0.181 2128 Planarity : 0.006 0.069 1385 Dihedral : 30.361 81.131 4053 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.31 % Allowed : 9.08 % 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: 2.78 (0.27), residues: 787 helix: 2.46 (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 0.005 0.001 ARG E 116 TYR 0.019 0.003 TYR F 51 PHE 0.009 0.002 PHE E 84 HIS 0.005 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00549 (12894) covalent geometry : angle 0.72284 (18709) hydrogen bonds : bond 0.07583 ( 799) hydrogen bonds : angle 3.49005 ( 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 136 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.360 Fit side-chains REVERT: D 72 GLU cc_start: 0.8623 (pp20) cc_final: 0.8360 (pp20) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 1.1991 time to fit residues: 168.5902 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 : 0.234 ------------------------------------------------------------------------------- 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: 0.8980 chunk 33 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4320 r_free = 0.4320 target = 0.209186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.163382 restraints weight = 40378.046| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 0.97 r_work: 0.3366 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 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 = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12894 Z= 0.189 Angle : 0.641 8.561 18709 Z= 0.387 Chirality : 0.038 0.132 2128 Planarity : 0.005 0.036 1385 Dihedral : 30.369 82.627 4053 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 2.99 (0.28), residues: 787 helix: 2.67 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -0.04 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 53 TYR 0.014 0.002 TYR F 51 PHE 0.012 0.002 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00376 (12894) covalent geometry : angle 0.64144 (18709) hydrogen bonds : bond 0.06198 ( 799) hydrogen bonds : angle 3.23676 ( 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 132 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.395 Fit side-chains REVERT: H 72 GLU cc_start: 0.8622 (pp20) cc_final: 0.8361 (pp20) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 1.2310 time to fit residues: 169.3419 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 : 0.310 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 45 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4305 r_free = 0.4305 target = 0.207445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.160664 restraints weight = 37434.666| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.00 r_work: 0.3331 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12894 Z= 0.247 Angle : 0.698 7.766 18709 Z= 0.414 Chirality : 0.041 0.168 2128 Planarity : 0.006 0.063 1385 Dihedral : 30.314 81.854 4053 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.59 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: 2.86 (0.28), residues: 787 helix: 2.54 (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 0.001 ARG E 116 TYR 0.019 0.002 TYR F 51 PHE 0.008 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00508 (12894) covalent geometry : angle 0.69838 (18709) hydrogen bonds : bond 0.07217 ( 799) hydrogen bonds : angle 3.42509 ( 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 136 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.358 Fit side-chains REVERT: D 72 GLU cc_start: 0.8596 (pp20) cc_final: 0.8376 (pp20) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 1.2341 time to fit residues: 173.5073 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 : 0.361 ------------------------------------------------------------------------------- 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: 0.7980 chunk 83 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4321 r_free = 0.4321 target = 0.209346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.163193 restraints weight = 44156.909| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.01 r_work: 0.3362 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12894 Z= 0.184 Angle : 0.636 7.769 18709 Z= 0.385 Chirality : 0.038 0.130 2128 Planarity : 0.005 0.037 1385 Dihedral : 30.335 82.744 4053 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.09 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: 2.97 (0.28), residues: 787 helix: 2.63 (0.20), residues: 582 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 63 TYR 0.014 0.002 TYR F 51 PHE 0.011 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00366 (12894) covalent geometry : angle 0.63632 (18709) hydrogen bonds : bond 0.06204 ( 799) hydrogen bonds : angle 3.22154 ( 2003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7835.92 seconds wall clock time: 133 minutes 15.33 seconds (7995.33 seconds total)