Starting phenix.real_space_refine on Wed Mar 13 00:36:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e43_27878/03_2024/8e43_27878_neut_trim_updated.pdb" } resolution = 2.09 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= -0.022 sd= 0.948 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 P 3021 5.49 5 S 28 5.16 5 C 34658 2.51 5 N 13703 2.21 5 O 22619 1.98 5 F 2 1.80 5 H 41874 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ARG 189": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 221": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 22": "OD1" <-> "OD2" Residue "M TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "N ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 131": "OD1" <-> "OD2" Residue "N ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 200": "OD1" <-> "OD2" Residue "O ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 67": "OD1" <-> "OD2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 109": "OD1" <-> "OD2" Residue "P ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 115905 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93458 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 93265 Classifications: {'RNA': 2897} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 2897, 93265 Classifications: {'RNA': 2897} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 438, 'rna3p': 2458} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 100517 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3170 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3182 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "O" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "P" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1775 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 898 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 794 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 108 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 54 Unusual residues: {'UI0': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 54 Unusual residues: {'UI0': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" P A G I2505 " occ=0.50 ... (66 atoms not shown) pdb=" H22B G I2505 " occ=0.50 residue: pdb=" P A U I2506 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B U I2506 " occ=0.50 residue: pdb=" P A C I2507 " occ=0.50 ... (60 atoms not shown) pdb=" H6 B C I2507 " occ=0.50 residue: pdb=" P A C I2601 " occ=0.50 ... (60 atoms not shown) pdb=" H6 B C I2601 " occ=0.50 residue: pdb=" P A A I2602 " occ=0.50 ... (64 atoms not shown) pdb=" H2 B A I2602 " occ=0.50 residue: pdb=" P A G I2603 " occ=0.50 ... (66 atoms not shown) pdb=" H22B G I2603 " occ=0.50 residue: pdb=" C1 AUI0 I3001 " occ=0.50 ... (106 atoms not shown) pdb=" O8 BUI0 I3001 " occ=0.50 Time building chain proxies: 69.51, per 1000 atoms: 0.60 Number of scatterers: 115905 At special positions: 0 Unit cell: (228.83, 222.221, 190.003, 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) S 28 16.00 P 3021 15.00 F 2 9.00 O 22619 8.00 N 13703 7.00 C 34658 6.00 H 41874 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 85.83 Conformation dependent library (CDL) restraints added in 2.1 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 32 helices and 16 sheets defined 28.0% alpha, 19.0% beta 932 base pairs and 1645 stacking pairs defined. Time for finding SS restraints: 62.85 Creating SS restraints... Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.887A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 35' Processing helix chain 'K' and resid 131 through 136 removed outlier: 3.573A pdb=" N ILE K 135 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Proline residue: K 136 - end of helix No H-bonds generated for 'chain 'K' and resid 131 through 136' Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.946A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.578A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 7.120A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.957A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.571A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.626A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 41 removed outlier: 3.738A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 removed outlier: 6.749A pdb=" N THR M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.544A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.432A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.515A pdb=" N PHE M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.765A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.811A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.348A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASP N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 98 through 103' Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'O' and resid 24 through 38 removed outlier: 4.216A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.288A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 123 removed outlier: 3.872A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS O 123 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.702A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 removed outlier: 3.613A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR P 38 " --> pdb=" O ASP P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.892A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.676A pdb=" N HIS Q 19 " --> pdb=" O MET Q 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 16 Processing helix chain 'R' and resid 17 through 24 removed outlier: 4.305A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 2 through 8 removed outlier: 6.121A pdb=" N VAL K 16 " --> pdb=" O CYS K 6 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG K 14 " --> pdb=" O PRO K 8 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.710A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.055A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.313A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 1 through 6 removed outlier: 3.939A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 42 through 46 removed outlier: 4.121A pdb=" N GLY M 42 " --> pdb=" O GLN M 90 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ARG M 44 " --> pdb=" O ARG M 88 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG M 88 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLN M 46 " --> pdb=" O ALA M 86 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ALA M 86 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.680A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 11 through 16 removed outlier: 3.940A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER N 199 " --> pdb=" O LYS N 8 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU N 168 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 36 through 40 removed outlier: 3.932A pdb=" N LEU N 40 " --> pdb=" O TYR N 45 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR N 45 " --> pdb=" O LEU N 40 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 179 through 182 Processing sheet with id= 11, first strand: chain 'N' and resid 24 through 28 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'N' and resid 46 through 51 removed outlier: 6.289A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU N 84 " --> pdb=" O ARG N 46 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'N' and resid 105 through 108 removed outlier: 6.224A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'O' and resid 14 through 19 Processing sheet with id= 15, first strand: chain 'P' and resid 2 through 8 Processing sheet with id= 16, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.653A pdb=" N SER Q 29 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS Q 37 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP Q 31 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2365 hydrogen bonds 3830 hydrogen bond angles 0 basepair planarities 932 basepair parallelities 1648 stacking parallelities Total time for adding SS restraints: 145.46 Time building geometry restraints manager: 89.91 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: 41872 1.03 - 1.22: 629 1.22 - 1.42: 38237 1.42 - 1.61: 43022 1.61 - 1.80: 58 Bond restraints: 123818 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.408 0.394 2.00e-02 2.50e+03 3.87e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.84e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.362 0.273 2.00e-02 2.50e+03 1.86e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C11BUI0 I3001 " pdb=" C14BUI0 I3001 " ideal model delta sigma weight residual 1.586 1.347 0.239 2.00e-02 2.50e+03 1.42e+02 ... (remaining 123813 not shown) Histogram of bond angle deviations from ideal: 72.76 - 85.43: 3 85.43 - 98.09: 1 98.09 - 110.76: 111755 110.76 - 123.43: 93700 123.43 - 136.09: 16259 Bond angle restraints: 221718 Sorted by residual: angle pdb=" OP1B G I2505 " pdb=" P B G I2505 " pdb=" OP2B G I2505 " ideal model delta sigma weight residual 119.60 78.45 41.15 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C23BUI0 I3001 " pdb=" C34BUI0 I3001 " pdb=" C35BUI0 I3001 " ideal model delta sigma weight residual 85.79 125.33 -39.54 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C23AUI0 I3001 " pdb=" C34AUI0 I3001 " pdb=" C35AUI0 I3001 " ideal model delta sigma weight residual 85.79 125.21 -39.42 3.00e+00 1.11e-01 1.73e+02 angle pdb=" O3* PSU I2504 " pdb=" P B G I2505 " pdb=" OP1B G I2505 " ideal model delta sigma weight residual 108.00 72.76 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C15BUI0 I3001 " pdb=" C13BUI0 I3001 " pdb=" N2 BUI0 I3001 " ideal model delta sigma weight residual 89.79 122.50 -32.71 3.00e+00 1.11e-01 1.19e+02 ... (remaining 221713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 53980 36.00 - 72.00: 7391 72.00 - 108.00: 800 108.00 - 144.00: 16 144.00 - 179.99: 137 Dihedral angle restraints: 62324 sinusoidal: 58674 harmonic: 3650 Sorted by residual: dihedral pdb=" CA THR N 151 " pdb=" C THR N 151 " pdb=" N PRO N 152 " pdb=" CA PRO N 152 " ideal model delta harmonic sigma weight residual -180.00 -138.33 -41.67 0 5.00e+00 4.00e-02 6.94e+01 dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.88 -179.88 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 39.91 -167.91 1 1.70e+01 3.46e-03 6.57e+01 ... (remaining 62321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 16228 0.075 - 0.151: 216 0.151 - 0.226: 4 0.226 - 0.301: 1 0.301 - 0.377: 3 Chirality restraints: 16452 Sorted by residual: chirality pdb=" C16BUI0 I3001 " pdb=" C14BUI0 I3001 " pdb=" C18BUI0 I3001 " pdb=" C24BUI0 I3001 " both_signs ideal model delta sigma weight residual False -2.78 -2.40 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C16AUI0 I3001 " pdb=" C14AUI0 I3001 " pdb=" C18AUI0 I3001 " pdb=" C24AUI0 I3001 " both_signs ideal model delta sigma weight residual False -2.78 -2.40 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C2 AUI0 I3001 " pdb=" C3 AUI0 I3001 " pdb=" C39AUI0 I3001 " pdb=" F1 AUI0 I3001 " both_signs ideal model delta sigma weight residual False -2.47 -2.16 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 16449 not shown) Planarity restraints: 8179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.041 2.00e-02 2.50e+03 5.87e-01 7.76e+03 pdb=" C4' OMG I2251 " 0.440 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.671 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.591 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.206 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.923 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.219 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.900 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.025 2.00e-02 2.50e+03 5.85e-01 7.71e+03 pdb=" C4' 2MG I2445 " -0.453 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.708 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.584 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.570 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.221 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.887 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.214 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.911 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.016 2.00e-02 2.50e+03 5.79e-01 7.55e+03 pdb=" C4' OMC I2498 " 0.443 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.716 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.589 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.546 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.229 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.871 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.217 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.900 2.00e-02 2.50e+03 ... (remaining 8176 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 3758 2.13 - 2.75: 143986 2.75 - 3.37: 285106 3.37 - 3.98: 450663 3.98 - 4.60: 639147 Nonbonded interactions: 1522660 Sorted by model distance: nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.517 1.850 nonbonded pdb=" O ALA K 170 " pdb=" H ALA K 186 " model vdw 1.534 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.547 1.850 nonbonded pdb=" H21 G I2857 " pdb=" OP2 A I2860 " model vdw 1.552 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.568 1.850 ... (remaining 1522655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.880 Extract box with map and model: 28.870 Check model and map are aligned: 1.300 Set scattering table: 0.800 Process input model: 460.420 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.290 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: 0.020 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 510.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 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 : 0.006 0.394 81944 Z= 0.378 Angle : 0.568 41.145 125806 Z= 0.248 Chirality : 0.027 0.377 16452 Planarity : 0.022 0.587 4647 Dihedral : 23.484 179.884 50648 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.90 % Favored : 94.75 % Rotamer: Outliers : 1.06 % Allowed : 8.60 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.21), residues: 1163 helix: -1.72 (0.26), residues: 246 sheet: -1.54 (0.32), residues: 229 loop : -2.09 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 78 HIS 0.003 0.001 HIS K 200 PHE 0.006 0.001 PHE K 240 TYR 0.007 0.001 TYR L 58 ARG 0.002 0.000 ARG K 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 292 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 35 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7918 (mt-10) REVERT: K 72 ASP cc_start: 0.8580 (m-30) cc_final: 0.8361 (m-30) REVERT: K 114 ASP cc_start: 0.8219 (m-30) cc_final: 0.8002 (m-30) REVERT: K 135 ILE cc_start: 0.9346 (mm) cc_final: 0.9128 (mt) REVERT: L 118 THR cc_start: 0.9268 (t) cc_final: 0.9060 (p) REVERT: M 176 ASP cc_start: 0.8063 (p0) cc_final: 0.7844 (p0) REVERT: M 184 ASP cc_start: 0.8200 (m-30) cc_final: 0.7979 (m-30) REVERT: M 194 LYS cc_start: 0.8946 (mptp) cc_final: 0.8510 (mptp) REVERT: N 13 ARG cc_start: 0.5693 (ptp-170) cc_final: 0.5025 (ptm160) REVERT: O 106 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8669 (ttmt) outliers start: 10 outliers final: 8 residues processed: 298 average time/residue: 3.1587 time to fit residues: 1174.1512 Evaluate side-chains 240 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 232 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 246 THR Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 4.9990 chunk 325 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 376 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN K 163 GLN K 200 HIS L 54 GLN L 93 ASN L 104 GLN M 41 GLN M 115 GLN N 126 ASN N 173 GLN O 135 GLN P 31 GLN Q 6 ASN R 29 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 81944 Z= 0.340 Angle : 0.656 43.014 125806 Z= 0.338 Chirality : 0.037 0.306 16452 Planarity : 0.007 0.141 4647 Dihedral : 23.422 179.703 48422 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.73 % Favored : 94.93 % Rotamer: Outliers : 2.23 % Allowed : 14.12 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1163 helix: 0.00 (0.31), residues: 258 sheet: -1.10 (0.32), residues: 239 loop : -1.55 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.010 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.005 0.001 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8292 (m-30) cc_final: 0.8056 (m-30) REVERT: L 118 THR cc_start: 0.9290 (t) cc_final: 0.9033 (p) REVERT: M 176 ASP cc_start: 0.7454 (p0) cc_final: 0.7226 (p0) REVERT: N 13 ARG cc_start: 0.5872 (ptp-170) cc_final: 0.5222 (ptm160) REVERT: O 106 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8779 (ttmt) REVERT: P 92 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7512 (ttp-170) outliers start: 21 outliers final: 12 residues processed: 244 average time/residue: 2.9653 time to fit residues: 922.5600 Evaluate side-chains 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 28 LYS Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 15 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 374 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN L 104 GLN M 115 GLN N 94 GLN N 126 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 81944 Z= 0.278 Angle : 0.573 14.416 125806 Z= 0.315 Chirality : 0.035 0.288 16452 Planarity : 0.007 0.137 4647 Dihedral : 23.395 177.665 48420 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.07 % Favored : 94.50 % Rotamer: Outliers : 1.27 % Allowed : 14.86 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.09 % 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: -0.90 (0.24), residues: 1163 helix: 0.78 (0.33), residues: 258 sheet: -0.73 (0.34), residues: 204 loop : -1.10 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.007 0.001 TYR Q 49 ARG 0.005 0.001 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8243 (m-30) cc_final: 0.8003 (m-30) REVERT: L 118 THR cc_start: 0.9283 (t) cc_final: 0.9047 (p) REVERT: N 13 ARG cc_start: 0.5915 (ptp-170) cc_final: 0.5215 (ptm160) REVERT: N 161 MET cc_start: 0.9468 (mtt) cc_final: 0.9074 (mtt) outliers start: 12 outliers final: 10 residues processed: 230 average time/residue: 2.9487 time to fit residues: 868.2717 Evaluate side-chains 218 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 359 optimal weight: 5.9990 chunk 108 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN K 163 GLN L 104 GLN M 115 GLN P 31 GLN R 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 81944 Z= 0.408 Angle : 0.631 14.845 125806 Z= 0.343 Chirality : 0.040 0.298 16452 Planarity : 0.007 0.141 4647 Dihedral : 23.413 179.252 48420 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.16 % Favored : 94.41 % Rotamer: Outliers : 1.91 % Allowed : 15.61 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % 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: -0.69 (0.24), residues: 1163 helix: 0.95 (0.33), residues: 261 sheet: -0.61 (0.33), residues: 227 loop : -0.96 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR Q 49 ARG 0.005 0.001 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8329 (m-30) cc_final: 0.8101 (m-30) REVERT: L 118 THR cc_start: 0.9288 (t) cc_final: 0.9011 (p) REVERT: M 6 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8330 (ttpp) REVERT: N 13 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5306 (ptm160) REVERT: N 161 MET cc_start: 0.9465 (mtt) cc_final: 0.9115 (mtt) REVERT: P 70 LYS cc_start: 0.8631 (tttt) cc_final: 0.8422 (tttm) outliers start: 18 outliers final: 12 residues processed: 220 average time/residue: 2.9443 time to fit residues: 826.4129 Evaluate side-chains 228 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 215 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 360 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN K 163 GLN L 104 GLN N 94 GLN P 31 GLN R 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 81944 Z= 0.316 Angle : 0.608 14.674 125806 Z= 0.334 Chirality : 0.036 0.293 16452 Planarity : 0.007 0.138 4647 Dihedral : 23.431 179.018 48420 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.33 % Favored : 94.24 % Rotamer: Outliers : 1.91 % Allowed : 15.92 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.09 % 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: -0.55 (0.24), residues: 1163 helix: 1.18 (0.33), residues: 255 sheet: -0.55 (0.33), residues: 227 loop : -0.90 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.013 0.001 PHE K 240 TYR 0.010 0.001 TYR Q 49 ARG 0.008 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8325 (m-30) cc_final: 0.8095 (m-30) REVERT: L 118 THR cc_start: 0.9266 (t) cc_final: 0.9018 (p) REVERT: L 136 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: M 6 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8310 (ttpp) REVERT: N 13 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.5333 (ptm160) REVERT: P 70 LYS cc_start: 0.8619 (tttt) cc_final: 0.8412 (tttm) outliers start: 18 outliers final: 14 residues processed: 226 average time/residue: 2.9186 time to fit residues: 845.8536 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 15 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 6.9990 chunk 333 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 210 optimal weight: 50.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN K 163 GLN L 104 GLN M 115 GLN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 81944 Z= 0.348 Angle : 0.599 14.637 125806 Z= 0.328 Chirality : 0.037 0.295 16452 Planarity : 0.007 0.136 4647 Dihedral : 23.438 177.935 48420 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.67 % Favored : 93.90 % Rotamer: Outliers : 2.34 % Allowed : 15.61 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.09 % 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: -0.43 (0.25), residues: 1163 helix: 1.23 (0.33), residues: 260 sheet: -0.45 (0.33), residues: 234 loop : -0.83 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.014 0.001 PHE K 240 TYR 0.009 0.001 TYR Q 49 ARG 0.008 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8286 (m-30) cc_final: 0.8038 (m-30) REVERT: L 118 THR cc_start: 0.9275 (t) cc_final: 0.9028 (p) REVERT: M 6 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8330 (ttpp) REVERT: N 13 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5393 (ptm160) REVERT: N 161 MET cc_start: 0.9476 (mtt) cc_final: 0.9159 (mtt) outliers start: 22 outliers final: 17 residues processed: 224 average time/residue: 2.9608 time to fit residues: 851.1228 Evaluate side-chains 236 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 28 LYS Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 15 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN L 104 GLN M 115 GLN M 195 GLN N 94 GLN N 126 ASN P 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 81944 Z= 0.322 Angle : 0.592 14.500 125806 Z= 0.325 Chirality : 0.037 0.290 16452 Planarity : 0.007 0.136 4647 Dihedral : 23.440 177.883 48420 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.59 % Favored : 93.98 % Rotamer: Outliers : 2.02 % Allowed : 16.67 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.09 % 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: -0.30 (0.25), residues: 1163 helix: 1.24 (0.33), residues: 266 sheet: -0.36 (0.34), residues: 227 loop : -0.72 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS O 76 PHE 0.013 0.001 PHE K 240 TYR 0.011 0.001 TYR Q 49 ARG 0.004 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8304 (m-30) cc_final: 0.8068 (m-30) REVERT: L 118 THR cc_start: 0.9277 (t) cc_final: 0.9046 (p) REVERT: L 136 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: N 13 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5398 (ptm160) REVERT: N 161 MET cc_start: 0.9472 (mtt) cc_final: 0.9154 (mtt) outliers start: 19 outliers final: 15 residues processed: 229 average time/residue: 3.0261 time to fit residues: 877.8634 Evaluate side-chains 236 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 219 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN L 104 GLN M 195 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 81944 Z= 0.342 Angle : 0.601 14.539 125806 Z= 0.330 Chirality : 0.037 0.290 16452 Planarity : 0.007 0.137 4647 Dihedral : 23.446 178.152 48420 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.59 % Favored : 93.98 % Rotamer: Outliers : 2.02 % Allowed : 16.77 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.09 % 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: -0.27 (0.25), residues: 1163 helix: 1.26 (0.32), residues: 266 sheet: -0.44 (0.34), residues: 225 loop : -0.65 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS O 76 PHE 0.014 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.004 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8280 (m-30) cc_final: 0.8042 (m-30) REVERT: L 118 THR cc_start: 0.9292 (t) cc_final: 0.9068 (p) REVERT: N 13 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.5490 (ptm160) REVERT: N 161 MET cc_start: 0.9478 (mtt) cc_final: 0.9177 (mtt) outliers start: 19 outliers final: 16 residues processed: 224 average time/residue: 2.9242 time to fit residues: 835.2401 Evaluate side-chains 235 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 218 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 4.9990 chunk 383 optimal weight: 4.9990 chunk 349 optimal weight: 0.6980 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 chunk 371 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN K 163 GLN L 104 GLN M 115 GLN M 195 GLN N 94 GLN O 138 GLN P 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 81944 Z= 0.313 Angle : 0.595 14.495 125806 Z= 0.328 Chirality : 0.036 0.288 16452 Planarity : 0.007 0.136 4647 Dihedral : 23.454 178.163 48420 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.50 % Favored : 94.07 % Rotamer: Outliers : 1.70 % Allowed : 17.52 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.09 % 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: -0.25 (0.25), residues: 1163 helix: 1.28 (0.32), residues: 266 sheet: -0.41 (0.33), residues: 232 loop : -0.65 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.013 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.004 0.000 ARG M 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 220 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8280 (m-30) cc_final: 0.8041 (m-30) REVERT: L 118 THR cc_start: 0.9294 (t) cc_final: 0.9074 (p) REVERT: N 13 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5485 (ptm160) REVERT: N 161 MET cc_start: 0.9475 (mtt) cc_final: 0.9182 (mtt) outliers start: 16 outliers final: 16 residues processed: 229 average time/residue: 2.9775 time to fit residues: 865.6027 Evaluate side-chains 229 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 212 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 70 LYS Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 2.9990 chunk 394 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 413 optimal weight: 0.6980 chunk 380 optimal weight: 0.7980 chunk 329 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN K 163 GLN L 104 GLN M 195 GLN N 94 GLN P 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 81944 Z= 0.182 Angle : 0.575 14.387 125806 Z= 0.321 Chirality : 0.032 0.283 16452 Planarity : 0.007 0.133 4647 Dihedral : 23.490 178.134 48420 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.67 % Favored : 93.90 % Rotamer: Outliers : 1.80 % Allowed : 17.41 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.09 % 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: -0.21 (0.25), residues: 1163 helix: 1.31 (0.32), residues: 266 sheet: -0.39 (0.34), residues: 209 loop : -0.61 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.012 0.001 PHE K 240 TYR 0.009 0.001 TYR Q 49 ARG 0.003 0.000 ARG R 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 214 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.8267 (m-30) cc_final: 0.8033 (m-30) REVERT: L 118 THR cc_start: 0.9296 (t) cc_final: 0.9079 (p) REVERT: N 13 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5464 (ptm160) REVERT: N 161 MET cc_start: 0.9470 (mtt) cc_final: 0.9173 (mtt) outliers start: 17 outliers final: 17 residues processed: 222 average time/residue: 2.9989 time to fit residues: 851.7523 Evaluate side-chains 237 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 219 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 70 LYS Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 338 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN K 163 GLN M 115 GLN M 195 GLN N 94 GLN P 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.062288 restraints weight = 359714.263| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 0.65 r_work: 0.2543 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 81944 Z= 0.356 Angle : 0.606 14.564 125806 Z= 0.332 Chirality : 0.038 0.287 16452 Planarity : 0.007 0.139 4647 Dihedral : 23.439 178.307 48420 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.50 % Favored : 94.07 % Rotamer: Outliers : 1.70 % Allowed : 17.52 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.09 % 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: -0.27 (0.25), residues: 1163 helix: 1.24 (0.32), residues: 267 sheet: -0.41 (0.33), residues: 232 loop : -0.66 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR Q 49 ARG 0.003 0.000 ARG Q 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37766.66 seconds wall clock time: 648 minutes 15.80 seconds (38895.80 seconds total)