Starting phenix.real_space_refine on Sat Sep 28 05:06:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/09_2024/6s61_10101.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/09_2024/6s61_10101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/09_2024/6s61_10101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/09_2024/6s61_10101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/09_2024/6s61_10101.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/09_2024/6s61_10101.cif" } resolution = 1.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 24 6.06 5 S 192 5.16 5 C 21456 2.51 5 N 6048 2.21 5 O 10430 1.98 5 H 32904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 71060 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 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: 2758 Chain: "E" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 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: 2758 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "E" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "F" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "G" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "H" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "I" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "J" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "K" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "L" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "M" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "N" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "O" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "P" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "Q" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "R" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "S" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "T" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "U" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "V" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "W" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Restraints were copied for chains: G, F, H, K, J, M, L, O, N, P, S, R, U, T, W, V, X, C, B, D, I, Q Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER A 113 " occ=0.30 residue: pdb=" N ASER B 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER B 113 " occ=0.30 residue: pdb=" N ASER C 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER C 113 " occ=0.30 residue: pdb=" N ASER D 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER D 113 " occ=0.30 residue: pdb=" N ASER E 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER E 113 " occ=0.30 residue: pdb=" N ASER F 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER F 113 " occ=0.30 residue: pdb=" N ASER G 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER G 113 " occ=0.30 residue: pdb=" N ASER H 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER H 113 " occ=0.30 residue: pdb=" N ASER I 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER I 113 " occ=0.30 residue: pdb=" N ASER J 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER J 113 " occ=0.30 residue: pdb=" N ASER K 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER K 113 " occ=0.30 residue: pdb=" N ASER L 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER L 113 " occ=0.30 ... (remaining 44 not shown) Time building chain proxies: 18.87, per 1000 atoms: 0.27 Number of scatterers: 71060 At special positions: 0 Unit cell: (134.48, 134.48, 134.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 24 29.99 Fe 6 26.01 S 192 16.00 O 10430 8.00 N 6048 7.00 C 21456 6.00 H 32904 1.00 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: 14.48 Conformation dependent library (CDL) restraints added in 10.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 201 " pdb="ZN ZN O 201 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" ND1 HIS X 65 " 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 8040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.63 Time building geometry restraints manager: 17.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32808 1.03 - 1.23: 2040 1.23 - 1.42: 13296 1.42 - 1.62: 19464 1.62 - 1.81: 312 Bond restraints: 67920 Sorted by residual: bond pdb=" CA ARG U 63 " pdb=" HA ARG U 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG G 63 " pdb=" HA ARG G 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG L 63 " pdb=" HA ARG L 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG E 63 " pdb=" HA ARG E 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG F 63 " pdb=" HA ARG F 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 ... (remaining 67915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 115608 2.34 - 4.67: 5928 4.67 - 7.01: 504 7.01 - 9.35: 144 9.35 - 11.69: 24 Bond angle restraints: 122208 Sorted by residual: angle pdb=" N ARG I 63 " pdb=" CA ARG I 63 " pdb=" C ARG I 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG J 63 " pdb=" CA ARG J 63 " pdb=" C ARG J 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG M 63 " pdb=" CA ARG M 63 " pdb=" C ARG M 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG X 63 " pdb=" CA ARG X 63 " pdb=" C ARG X 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG R 63 " pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 ... (remaining 122203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 29808 17.50 - 34.99: 1440 34.99 - 52.48: 480 52.48 - 69.98: 360 69.98 - 87.47: 24 Dihedral angle restraints: 32112 sinusoidal: 17232 harmonic: 14880 Sorted by residual: dihedral pdb=" CA VAL Q 46 " pdb=" C VAL Q 46 " pdb=" N ALA Q 47 " pdb=" CA ALA Q 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL P 46 " pdb=" C VAL P 46 " pdb=" N ALA P 47 " pdb=" CA ALA P 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 32109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3168 0.047 - 0.093: 1128 0.093 - 0.140: 408 0.140 - 0.186: 120 0.186 - 0.232: 96 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA ASN P 50 " pdb=" N ASN P 50 " pdb=" C ASN P 50 " pdb=" CB ASN P 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN H 50 " pdb=" N ASN H 50 " pdb=" C ASN H 50 " pdb=" CB ASN H 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN B 50 " pdb=" N ASN B 50 " pdb=" C ASN B 50 " pdb=" CB ASN B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4917 not shown) Planarity restraints: 10344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN S 75 " 0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN S 75 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN S 75 " -0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN S 75 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN S 75 " -0.495 2.00e-02 2.50e+03 pdb="HE22 GLN S 75 " 0.495 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN V 75 " -0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN V 75 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN V 75 " 0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN V 75 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN V 75 " 0.495 2.00e-02 2.50e+03 pdb="HE22 GLN V 75 " -0.495 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 75 " 0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN F 75 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN F 75 " -0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN F 75 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN F 75 " -0.495 2.00e-02 2.50e+03 pdb="HE22 GLN F 75 " 0.495 2.00e-02 2.50e+03 ... (remaining 10341 not shown) Histogram of nonbonded interaction distances: 0.31 - 1.17: 168 1.17 - 2.03: 1776 2.03 - 2.88: 180624 2.88 - 3.74: 350652 3.74 - 4.60: 593820 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1127040 Sorted by model distance: nonbonded pdb=" NH2BARG O 63 " pdb=" NH2BARG V 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG E 63 " pdb=" NH2BARG U 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG H 63 " pdb=" NH2BARG S 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG F 63 " pdb=" NH2BARG Q 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG G 63 " pdb=" NH2BARG X 63 " model vdw 0.312 3.100 ... (remaining 1127035 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 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'B' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'C' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'D' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'E' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'F' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'G' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'H' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'I' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'J' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'K' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'L' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'M' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'N' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'O' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'P' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'Q' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'R' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'S' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'T' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'U' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'V' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'W' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'X' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) } 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=0.15 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: 0.010 Normalize map: mean=0, sd=1: 1.820 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: 1.400 Extract box with map and model: 2.210 Check model and map are aligned: 0.410 Set scattering table: 0.510 Process input model: 138.470 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.011 0.088 35016 Z= 0.731 Angle : 1.356 8.395 47160 Z= 0.990 Chirality : 0.063 0.232 4920 Planarity : 0.010 0.046 6216 Dihedral : 12.210 87.470 13344 Min Nonbonded Distance : 0.312 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.29 % Allowed : 2.58 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.12), residues: 4224 helix: 2.89 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.60 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP F 93 HIS 0.013 0.005 HIS U 151 PHE 0.032 0.007 PHE R 41 TYR 0.080 0.007 TYR A 32 ARG 0.010 0.001 ARG P 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 984 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 936 time to evaluate : 4.553 Fit side-chains REVERT: A 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: B 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: C 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8737 (mmt) REVERT: D 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8741 (mmt) REVERT: E 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8732 (mmt) REVERT: F 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8735 (mmt) REVERT: G 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8743 (mmt) REVERT: H 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: I 100 MET cc_start: 0.9068 (mmt) cc_final: 0.8742 (mmt) REVERT: J 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8736 (mmt) REVERT: K 100 MET cc_start: 0.9068 (mmt) cc_final: 0.8742 (mmt) REVERT: L 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8743 (mmt) REVERT: M 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8742 (mmt) REVERT: N 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8737 (mmt) REVERT: O 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8732 (mmt) REVERT: P 100 MET cc_start: 0.9064 (mmt) cc_final: 0.8738 (mmt) REVERT: Q 100 MET cc_start: 0.9064 (mmt) cc_final: 0.8738 (mmt) REVERT: R 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8737 (mmt) REVERT: S 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8732 (mmt) REVERT: T 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8736 (mmt) REVERT: U 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: V 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: W 100 MET cc_start: 0.9064 (mmt) cc_final: 0.8738 (mmt) REVERT: X 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) outliers start: 48 outliers final: 0 residues processed: 984 average time/residue: 3.5626 time to fit residues: 4076.0362 Evaluate side-chains 744 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 744 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.9980 chunk 309 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 370 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 83 GLN A 125 ASN A 141 GLN B 75 GLN B 83 GLN B 125 ASN B 141 GLN C 75 GLN C 83 GLN C 125 ASN C 141 GLN D 75 GLN D 83 GLN D 125 ASN D 141 GLN E 75 GLN E 83 GLN E 125 ASN E 141 GLN F 75 GLN F 83 GLN F 125 ASN F 141 GLN G 75 GLN G 83 GLN G 125 ASN G 141 GLN H 75 GLN H 83 GLN H 125 ASN H 141 GLN I 75 GLN I 83 GLN I 125 ASN I 141 GLN J 75 GLN J 83 GLN J 125 ASN J 141 GLN K 75 GLN K 83 GLN K 125 ASN K 141 GLN L 75 GLN L 83 GLN L 125 ASN L 141 GLN M 75 GLN M 83 GLN M 125 ASN M 141 GLN N 75 GLN N 83 GLN N 125 ASN N 141 GLN O 75 GLN O 83 GLN O 125 ASN O 141 GLN P 75 GLN P 83 GLN P 125 ASN P 141 GLN Q 75 GLN Q 83 GLN Q 125 ASN Q 141 GLN R 75 GLN R 83 GLN R 125 ASN R 141 GLN S 75 GLN S 83 GLN S 125 ASN S 141 GLN T 75 GLN T 83 GLN T 125 ASN T 141 GLN U 75 GLN U 83 GLN U 125 ASN U 141 GLN V 75 GLN V 83 GLN V 125 ASN V 141 GLN W 75 GLN W 83 GLN W 125 ASN W 141 GLN X 75 GLN X 83 GLN X 125 ASN X 141 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35016 Z= 0.177 Angle : 0.542 4.387 47160 Z= 0.298 Chirality : 0.033 0.124 4920 Planarity : 0.003 0.020 6216 Dihedral : 4.174 21.581 4632 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.13), residues: 4224 helix: 3.81 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.63 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 93 HIS 0.005 0.001 HIS L 60 PHE 0.009 0.002 PHE F 41 TYR 0.033 0.002 TYR F 32 ARG 0.002 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 840 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 840 time to evaluate : 4.651 Fit side-chains REVERT: A 100 MET cc_start: 0.9114 (mmt) cc_final: 0.8892 (mmt) REVERT: B 100 MET cc_start: 0.9114 (mmt) cc_final: 0.8892 (mmt) REVERT: C 100 MET cc_start: 0.9117 (mmt) cc_final: 0.8896 (mmt) REVERT: D 100 MET cc_start: 0.9112 (mmt) cc_final: 0.8894 (mmt) REVERT: E 100 MET cc_start: 0.9118 (mmt) cc_final: 0.8889 (mmt) REVERT: F 100 MET cc_start: 0.9123 (mmt) cc_final: 0.8894 (mmt) REVERT: G 100 MET cc_start: 0.9117 (mmt) cc_final: 0.8893 (mmt) REVERT: H 100 MET cc_start: 0.9113 (mmt) cc_final: 0.8889 (mmt) REVERT: I 100 MET cc_start: 0.9112 (mmt) cc_final: 0.8895 (mmt) REVERT: J 100 MET cc_start: 0.9123 (mmt) cc_final: 0.8894 (mmt) REVERT: K 100 MET cc_start: 0.9112 (mmt) cc_final: 0.8895 (mmt) REVERT: L 100 MET cc_start: 0.9117 (mmt) cc_final: 0.8894 (mmt) REVERT: M 100 MET cc_start: 0.9117 (mmt) cc_final: 0.8893 (mmt) REVERT: N 100 MET cc_start: 0.9117 (mmt) cc_final: 0.8896 (mmt) REVERT: O 100 MET cc_start: 0.9118 (mmt) cc_final: 0.8889 (mmt) REVERT: P 100 MET cc_start: 0.9110 (mmt) cc_final: 0.8892 (mmt) REVERT: Q 100 MET cc_start: 0.9110 (mmt) cc_final: 0.8892 (mmt) REVERT: R 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8895 (mmt) REVERT: S 100 MET cc_start: 0.9118 (mmt) cc_final: 0.8889 (mmt) REVERT: T 100 MET cc_start: 0.9123 (mmt) cc_final: 0.8894 (mmt) REVERT: U 100 MET cc_start: 0.9113 (mmt) cc_final: 0.8889 (mmt) REVERT: V 100 MET cc_start: 0.9113 (mmt) cc_final: 0.8889 (mmt) REVERT: W 100 MET cc_start: 0.9110 (mmt) cc_final: 0.8892 (mmt) REVERT: X 100 MET cc_start: 0.9114 (mmt) cc_final: 0.8892 (mmt) outliers start: 0 outliers final: 0 residues processed: 840 average time/residue: 4.1061 time to fit residues: 3933.8851 Evaluate side-chains 649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 649 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 105 HIS M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 105 HIS Q 141 GLN R 141 GLN S 105 HIS S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 35016 Z= 0.317 Angle : 0.673 5.575 47160 Z= 0.380 Chirality : 0.039 0.129 4920 Planarity : 0.005 0.034 6216 Dihedral : 4.212 19.396 4632 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.03 % Allowed : 7.72 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.13), residues: 4224 helix: 3.15 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.48 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.004 TRP K 93 HIS 0.008 0.003 HIS U 57 PHE 0.024 0.004 PHE U 41 TYR 0.054 0.005 TYR K 32 ARG 0.002 0.000 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 667 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 666 time to evaluate : 4.809 Fit side-chains REVERT: A 100 MET cc_start: 0.9133 (mmt) cc_final: 0.8873 (mmt) REVERT: B 100 MET cc_start: 0.9132 (mmt) cc_final: 0.8873 (mmt) REVERT: C 100 MET cc_start: 0.9137 (mmt) cc_final: 0.8876 (mmt) REVERT: D 100 MET cc_start: 0.9135 (mmt) cc_final: 0.8721 (mmt) REVERT: E 100 MET cc_start: 0.9137 (mmt) cc_final: 0.8711 (mmt) REVERT: F 100 MET cc_start: 0.9140 (mmt) cc_final: 0.8875 (mmt) REVERT: G 100 MET cc_start: 0.9138 (mmt) cc_final: 0.8880 (mmt) REVERT: H 100 MET cc_start: 0.9133 (mmt) cc_final: 0.8873 (mmt) REVERT: I 100 MET cc_start: 0.9135 (mmt) cc_final: 0.8881 (mmt) REVERT: J 100 MET cc_start: 0.9139 (mmt) cc_final: 0.8875 (mmt) REVERT: K 100 MET cc_start: 0.9135 (mmt) cc_final: 0.8880 (mmt) REVERT: L 100 MET cc_start: 0.9139 (mmt) cc_final: 0.8881 (mmt) REVERT: M 100 MET cc_start: 0.9138 (mmt) cc_final: 0.8878 (mmt) REVERT: N 100 MET cc_start: 0.9137 (mmt) cc_final: 0.8876 (mmt) REVERT: O 100 MET cc_start: 0.9137 (mmt) cc_final: 0.8873 (mmt) REVERT: P 100 MET cc_start: 0.9129 (mmt) cc_final: 0.8876 (mmt) REVERT: Q 100 MET cc_start: 0.9130 (mmt) cc_final: 0.8874 (mmt) REVERT: R 100 MET cc_start: 0.9136 (mmt) cc_final: 0.8717 (mmt) REVERT: S 100 MET cc_start: 0.9137 (mmt) cc_final: 0.8873 (mmt) REVERT: T 100 MET cc_start: 0.9139 (mmt) cc_final: 0.8875 (mmt) REVERT: U 100 MET cc_start: 0.9133 (mmt) cc_final: 0.8874 (mmt) REVERT: V 100 MET cc_start: 0.9133 (mmt) cc_final: 0.8874 (mmt) REVERT: W 100 MET cc_start: 0.9130 (mmt) cc_final: 0.8874 (mmt) REVERT: X 100 MET cc_start: 0.9132 (mmt) cc_final: 0.8872 (mmt) outliers start: 1 outliers final: 1 residues processed: 667 average time/residue: 3.9870 time to fit residues: 3059.8162 Evaluate side-chains 668 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 667 time to evaluate : 4.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 139 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 2.9990 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 35016 Z= 0.211 Angle : 0.560 5.108 47160 Z= 0.312 Chirality : 0.034 0.126 4920 Planarity : 0.003 0.023 6216 Dihedral : 4.136 20.606 4632 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.62 % Allowed : 7.04 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.54 (0.13), residues: 4224 helix: 3.58 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.42 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP R 93 HIS 0.004 0.002 HIS A 128 PHE 0.018 0.003 PHE E 41 TYR 0.035 0.003 TYR Q 32 ARG 0.001 0.000 ARG J 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 713 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 690 time to evaluate : 4.561 Fit side-chains outliers start: 23 outliers final: 23 residues processed: 713 average time/residue: 3.7130 time to fit residues: 3060.1252 Evaluate side-chains 713 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 690 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 35016 Z= 0.291 Angle : 0.643 5.344 47160 Z= 0.360 Chirality : 0.037 0.127 4920 Planarity : 0.005 0.033 6216 Dihedral : 4.183 19.602 4632 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.65 % Allowed : 7.02 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.13), residues: 4224 helix: 3.23 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.004 TRP V 93 HIS 0.007 0.003 HIS G 57 PHE 0.024 0.004 PHE W 41 TYR 0.038 0.004 TYR K 32 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 711 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 687 time to evaluate : 4.580 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 711 average time/residue: 3.8154 time to fit residues: 3126.9602 Evaluate side-chains 699 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 675 time to evaluate : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 2.9990 chunk 355 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 394 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 35016 Z= 0.249 Angle : 0.594 5.148 47160 Z= 0.332 Chirality : 0.035 0.127 4920 Planarity : 0.004 0.029 6216 Dihedral : 4.161 19.911 4632 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.62 % Allowed : 7.69 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.31 (0.13), residues: 4224 helix: 3.41 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.41 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP K 93 HIS 0.005 0.002 HIS L 57 PHE 0.019 0.003 PHE R 41 TYR 0.031 0.003 TYR S 32 ARG 0.002 0.000 ARG S 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 695 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 672 time to evaluate : 4.788 Fit side-chains outliers start: 23 outliers final: 23 residues processed: 695 average time/residue: 3.7411 time to fit residues: 3001.8565 Evaluate side-chains 673 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 650 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 35016 Z= 0.262 Angle : 0.612 5.311 47160 Z= 0.342 Chirality : 0.036 0.127 4920 Planarity : 0.004 0.029 6216 Dihedral : 4.170 19.624 4632 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 7.74 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.13), residues: 4224 helix: 3.33 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.40 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP F 93 HIS 0.006 0.002 HIS N 57 PHE 0.022 0.003 PHE D 41 TYR 0.031 0.003 TYR L 32 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 699 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 675 time to evaluate : 4.634 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 699 average time/residue: 3.7468 time to fit residues: 3025.2321 Evaluate side-chains 673 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 649 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 35016 Z= 0.303 Angle : 0.647 5.382 47160 Z= 0.362 Chirality : 0.037 0.127 4920 Planarity : 0.004 0.030 6216 Dihedral : 4.182 19.153 4632 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.65 % Allowed : 7.74 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.13), residues: 4224 helix: 3.21 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.40 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.004 TRP C 93 HIS 0.008 0.003 HIS A 57 PHE 0.024 0.003 PHE B 41 TYR 0.031 0.003 TYR K 32 ARG 0.002 0.000 ARG T 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 674 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 650 time to evaluate : 4.518 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 674 average time/residue: 3.7737 time to fit residues: 2939.0960 Evaluate side-chains 671 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 647 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 0.7980 chunk 346 optimal weight: 5.9990 chunk 365 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 35016 Z= 0.190 Angle : 0.537 4.915 47160 Z= 0.298 Chirality : 0.034 0.124 4920 Planarity : 0.003 0.021 6216 Dihedral : 4.116 20.864 4632 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.62 % Allowed : 7.80 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.13), residues: 4224 helix: 3.77 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.55 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP W 93 HIS 0.004 0.001 HIS L 60 PHE 0.015 0.002 PHE I 41 TYR 0.020 0.002 TYR L 32 ARG 0.001 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 672 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 649 time to evaluate : 5.835 Fit side-chains outliers start: 23 outliers final: 23 residues processed: 672 average time/residue: 3.7663 time to fit residues: 2921.6857 Evaluate side-chains 669 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 646 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 0.7980 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 35016 Z= 0.219 Angle : 0.572 5.120 47160 Z= 0.319 Chirality : 0.035 0.124 4920 Planarity : 0.003 0.024 6216 Dihedral : 4.138 20.860 4632 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.65 % Allowed : 8.39 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.61 (0.13), residues: 4224 helix: 3.62 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.53 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP W 93 HIS 0.005 0.002 HIS D 57 PHE 0.018 0.003 PHE D 41 TYR 0.024 0.002 TYR B 32 ARG 0.002 0.000 ARG T 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 675 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 651 time to evaluate : 4.608 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 675 average time/residue: 3.7484 time to fit residues: 2922.8047 Evaluate side-chains 673 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 649 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.140116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.115881 restraints weight = 130879.659| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 0.63 r_work: 0.2965 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.2453 rms_B_bonded: 4.48 restraints_weight: 0.1250 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2401 r_free = 0.2401 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2400 r_free = 0.2400 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 35016 Z= 0.258 Angle : 0.611 5.222 47160 Z= 0.340 Chirality : 0.036 0.127 4920 Planarity : 0.004 0.028 6216 Dihedral : 4.147 20.019 4632 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.65 % Allowed : 7.80 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.13), residues: 4224 helix: 3.40 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.49 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.004 TRP T 93 HIS 0.006 0.002 HIS S 57 PHE 0.021 0.003 PHE K 41 TYR 0.027 0.003 TYR B 32 ARG 0.002 0.000 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40499.65 seconds wall clock time: 686 minutes 32.00 seconds (41192.00 seconds total)