Starting phenix.real_space_refine on Tue Mar 12 23:35:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/03_2024/8e48_27883_neut_trim_updated.pdb" } resolution = 2.27 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= 0.001 sd= 0.810 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 3025 5.49 5 S 28 5.16 5 C 34636 2.51 5 N 13719 2.21 5 O 22632 1.98 5 F 1 1.80 5 H 41918 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 72": "OD1" <-> "OD2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 194": "OE1" <-> "OE2" Residue "K GLU 199": "OE1" <-> "OE2" Residue "K GLU 236": "OE1" <-> "OE2" Residue "K ASP 264": "OD1" <-> "OD2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M GLU 197": "OE1" <-> "OE2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ASP 108": "OD1" <-> "OD2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O GLU 31": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "P GLU 2": "OE1" <-> "OE2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 78": "OE1" <-> "OE2" Residue "Q GLU 36": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 115959 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 278, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1387, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 436, 'rna3p': 2461} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1385, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2460} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 100447 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'UIF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UIF:plan-7': 1, 'UIF:plan-2': 1, 'UIF:plan-3': 1, 'UIF:plan-8': 1} Unresolved non-hydrogen planarities: 22 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" P A G I2061 " occ=0.50 ... (66 atoms not shown) pdb=" H22B G I2061 " occ=0.50 residue: pdb=" P A A I2062 " occ=0.50 ... (64 atoms not shown) pdb=" H2 B A I2062 " occ=0.50 residue: pdb=" P A C I2063 " occ=0.50 ... (60 atoms not shown) pdb=" H6 B C I2063 " occ=0.50 residue: pdb=" P A G I2505 " occ=0.54 ... (66 atoms not shown) pdb=" H22B G I2505 " occ=0.46 residue: pdb=" P A U I2506 " occ=0.54 ... (58 atoms not shown) pdb=" H6 B U I2506 " occ=0.46 residue: pdb=" P A C I2507 " occ=0.54 ... (60 atoms not shown) pdb=" H6 B C I2507 " occ=0.46 residue: pdb=" P A C I2601 " occ=0.57 ... (60 atoms not shown) pdb=" H6 B C I2601 " occ=0.43 residue: pdb=" P A A I2602 " occ=0.57 ... (64 atoms not shown) pdb=" H2 B A I2602 " occ=0.43 residue: pdb=" P A G I2603 " occ=0.57 ... (66 atoms not shown) pdb=" H22B G I2603 " occ=0.43 Time building chain proxies: 66.65, per 1000 atoms: 0.57 Number of scatterers: 115959 At special positions: 0 Unit cell: (232.085, 224.77, 193.515, 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 3025 15.00 F 1 9.00 O 22632 8.00 N 13719 7.00 C 34636 6.00 H 41918 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 70.57 Conformation dependent library (CDL) restraints added in 2.2 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: 37 helices and 11 sheets defined 30.7% alpha, 14.2% beta 571 base pairs and 1615 stacking pairs defined. Time for finding SS restraints: 53.55 Creating SS restraints... Processing helix chain 'K' and resid 12 through 17 removed outlier: 5.505A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 12 through 17' Processing helix chain 'K' and resid 30 through 35 removed outlier: 4.146A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.870A 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: 3.658A 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: 3.978A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.278A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 197 through 202 removed outlier: 4.152A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.565A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.757A 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: 7.011A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.260A 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 86 removed outlier: 3.979A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.636A 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 40 removed outlier: 3.695A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.500A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.667A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.560A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 removed outlier: 3.724A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 3.671A pdb=" N VAL N 60 " --> pdb=" O LYS N 56 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 61' Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.751A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.731A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.394A 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 'N' and resid 39 through 44 Processing helix chain 'O' and resid 24 through 38 removed outlier: 4.046A pdb=" N LEU O 28 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA O 29 " --> pdb=" O LEU O 25 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR O 30 " --> pdb=" O GLY O 26 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.303A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.635A 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 122 removed outlier: 3.512A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.785A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 40 removed outlier: 3.582A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR P 38 " --> pdb=" O ASP P 34 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR P 39 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.973A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 removed outlier: 3.868A pdb=" N LEU P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 70' Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.987A 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: 4.275A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 38 removed outlier: 3.507A pdb=" N LEU R 31 " --> pdb=" O GLY R 27 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.795A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.447A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.097A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'M' and resid 117 through 120 removed outlier: 6.123A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL M 146 " --> pdb=" O LYS M 166 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= 6, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.785A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'N' and resid 79 through 84 removed outlier: 3.520A pdb=" N LEU N 84 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'O' and resid 52 through 57 removed outlier: 5.063A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'O' and resid 74 through 78 removed outlier: 7.058A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'P' and resid 2 through 8 removed outlier: 4.743A pdb=" N THR P 100 " --> pdb=" O GLY P 79 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'Q' and resid 29 through 32 removed outlier: 4.866A pdb=" N GLU Q 36 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1324 hydrogen bonds 1968 hydrogen bond angles 0 basepair planarities 571 basepair parallelities 1620 stacking parallelities Total time for adding SS restraints: 128.59 Time building geometry restraints manager: 74.76 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: 41916 1.03 - 1.23: 631 1.23 - 1.42: 43380 1.42 - 1.62: 37899 1.62 - 1.81: 54 Bond restraints: 123880 Sorted by residual: bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.413 0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.414 0.388 2.00e-02 2.50e+03 3.77e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.371 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.350 -0.195 2.00e-02 2.50e+03 9.50e+01 ... (remaining 123875 not shown) Histogram of bond angle deviations from ideal: 27.62 - 51.63: 2 51.63 - 75.64: 19 75.64 - 99.66: 22 99.66 - 123.67: 206271 123.67 - 147.68: 15555 Bond angle restraints: 221869 Sorted by residual: angle pdb=" N7 G I1138 " pdb=" C5 G I1138 " pdb=" C4 G I1138 " ideal model delta sigma weight residual 110.80 27.62 83.18 3.00e+00 1.11e-01 7.69e+02 angle pdb=" N9 G I1138 " pdb=" C8 G I1138 " pdb=" N7 G I1138 " ideal model delta sigma weight residual 113.10 43.92 69.18 3.00e+00 1.11e-01 5.32e+02 angle pdb=" O3'B A I2062 " pdb=" C3'B A I2062 " pdb=" H3'B A I2062 " ideal model delta sigma weight residual 109.00 68.49 40.51 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C PRO L 56 " pdb=" CA PRO L 56 " pdb=" HA PRO L 56 " ideal model delta sigma weight residual 109.00 69.44 39.56 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C PRO R 7 " pdb=" CA PRO R 7 " pdb=" HA PRO R 7 " ideal model delta sigma weight residual 109.00 69.64 39.36 3.00e+00 1.11e-01 1.72e+02 ... (remaining 221864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 54953 35.38 - 70.75: 6616 70.75 - 106.13: 777 106.13 - 141.51: 5 141.51 - 176.89: 8 Dihedral angle restraints: 62359 sinusoidal: 58709 harmonic: 3650 Sorted by residual: dihedral pdb=" O4'A U I2506 " pdb=" C1'A U I2506 " pdb=" N1 A U I2506 " pdb=" C2 A U I2506 " ideal model delta sinusoidal sigma weight residual 232.00 55.11 176.89 1 1.70e+01 3.46e-03 6.64e+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 48.45 -176.45 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4'B C I2601 " pdb=" C1'B C I2601 " pdb=" N1 B C I2601 " pdb=" C2 B C I2601 " ideal model delta sinusoidal sigma weight residual 232.00 60.02 171.98 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 62356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 16448 0.209 - 0.419: 4 0.419 - 0.628: 1 0.628 - 0.837: 7 0.837 - 1.047: 1 Chirality restraints: 16461 Sorted by residual: chirality pdb=" C1' G I1138 " pdb=" O4' G I1138 " pdb=" C2' G I1138 " pdb=" N9 G I1138 " both_signs ideal model delta sigma weight residual False 2.46 1.41 1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" C1'B A I2602 " pdb=" O4'B A I2602 " pdb=" C2'B A I2602 " pdb=" N9 B A I2602 " both_signs ideal model delta sigma weight residual False 2.44 1.61 0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C4' G I1138 " pdb=" C5' G I1138 " pdb=" O4' G I1138 " pdb=" C3' G I1138 " both_signs ideal model delta sigma weight residual False -2.50 -1.67 -0.83 2.00e-01 2.50e+01 1.72e+01 ... (remaining 16458 not shown) Planarity restraints: 8175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.029 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' OMC I2498 " 0.452 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.746 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.576 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.225 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.893 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.207 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.934 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.040 2.00e-02 2.50e+03 5.72e-01 7.37e+03 pdb=" C4' 2MG I2445 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.619 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.576 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.918 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.231 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.867 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.042 2.00e-02 2.50e+03 5.69e-01 7.29e+03 pdb=" C4' OMG I2251 " 0.428 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.602 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.576 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.201 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.924 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.234 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.857 2.00e-02 2.50e+03 ... (remaining 8172 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 2288 2.09 - 2.72: 126249 2.72 - 3.35: 266083 3.35 - 3.97: 414172 3.97 - 4.60: 609193 Nonbonded interactions: 1417985 Sorted by model distance: nonbonded pdb=" O ASN O 128 " pdb="HD21 ASN O 128 " model vdw 1.465 1.850 nonbonded pdb=" H SER N 21 " pdb=" HA SER N 21 " model vdw 1.577 1.816 nonbonded pdb=" OE1 GLU L 10 " pdb=" H GLU L 10 " model vdw 1.608 1.850 nonbonded pdb=" O2 C I1728 " pdb=" H1 G I1731 " model vdw 1.613 1.850 nonbonded pdb=" H41 C I1838 " pdb=" OP2 A I1899 " model vdw 1.614 1.850 ... (remaining 1417980 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=0.43 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: 6.090 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: 0.900 Extract box with map and model: 30.310 Check model and map are aligned: 1.330 Set scattering table: 0.820 Process input model: 411.680 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.280 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 463.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.389 81962 Z= 0.302 Angle : 0.514 83.180 125857 Z= 0.231 Chirality : 0.029 1.047 16461 Planarity : 0.022 0.597 4639 Dihedral : 22.762 176.887 50674 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.53 % Allowed : 25.80 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.25), residues: 1163 helix: 1.43 (0.36), residues: 236 sheet: 0.93 (0.39), residues: 179 loop : -0.31 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP M 60 HIS 0.002 0.001 HIS K 230 PHE 0.005 0.001 PHE K 240 TYR 0.005 0.001 TYR L 58 ARG 0.007 0.000 ARG P 95 *********************** 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 246 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 241 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 111 LYS cc_start: 0.8168 (pttm) cc_final: 0.7930 (pttp) REVERT: K 114 ASP cc_start: 0.9032 (m-30) cc_final: 0.8798 (m-30) REVERT: O 12 LYS cc_start: 0.7241 (mmmm) cc_final: 0.6919 (mtpp) outliers start: 5 outliers final: 1 residues processed: 245 average time/residue: 3.3579 time to fit residues: 1016.1339 Evaluate side-chains 180 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 107 optimal weight: 50.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 376 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN N 126 ASN ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 81962 Z= 0.322 Angle : 0.770 83.992 125857 Z= 0.396 Chirality : 0.044 1.030 16461 Planarity : 0.007 0.144 4639 Dihedral : 22.556 176.715 48436 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 2.97 % Allowed : 22.72 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.24), residues: 1163 helix: 1.14 (0.33), residues: 257 sheet: 0.85 (0.41), residues: 157 loop : -0.80 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.008 0.001 HIS K 230 PHE 0.014 0.002 PHE M 183 TYR 0.012 0.002 TYR K 103 ARG 0.006 0.001 ARG O 34 *********************** 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 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 2.882 Fit side-chains revert: symmetry clash REVERT: M 21 ARG cc_start: 0.7776 (ptm160) cc_final: 0.7575 (ptm160) REVERT: M 152 GLU cc_start: 0.7346 (pm20) cc_final: 0.5664 (pp20) REVERT: O 12 LYS cc_start: 0.7851 (mmmm) cc_final: 0.7494 (mtpp) REVERT: O 142 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7604 (mp) REVERT: Q 28 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8525 (pp) outliers start: 28 outliers final: 6 residues processed: 210 average time/residue: 3.2380 time to fit residues: 846.0038 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 2.9990 chunk 407 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 374 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 302 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 136 GLN N 185 ASN O 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.171 81962 Z= 0.205 Angle : 0.660 83.532 125857 Z= 0.342 Chirality : 0.038 1.101 16461 Planarity : 0.006 0.134 4639 Dihedral : 22.525 176.413 48436 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 2.44 % Allowed : 22.82 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.24), residues: 1163 helix: 1.36 (0.34), residues: 257 sheet: 0.85 (0.38), residues: 172 loop : -0.95 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.012 0.001 PHE K 240 TYR 0.010 0.001 TYR O 75 ARG 0.005 0.000 ARG L 21 *********************** 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 216 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 3.228 Fit side-chains REVERT: K 182 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8669 (ttt90) REVERT: M 144 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7804 (mt-10) REVERT: N 1 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6492 (tmm) REVERT: N 99 GLU cc_start: 0.7709 (mp0) cc_final: 0.7499 (mp0) REVERT: O 142 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7605 (mp) REVERT: Q 28 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8652 (pp) REVERT: Q 30 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8801 (t) outliers start: 23 outliers final: 7 residues processed: 205 average time/residue: 3.2397 time to fit residues: 830.0418 Evaluate side-chains 192 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 4.9990 chunk 283 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 378 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 108 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 136 GLN P 61 ASN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.172 81962 Z= 0.383 Angle : 0.781 84.180 125857 Z= 0.401 Chirality : 0.045 1.097 16461 Planarity : 0.007 0.142 4639 Dihedral : 22.577 176.216 48436 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 2.87 % Allowed : 22.19 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.64 (0.23), residues: 1163 helix: 1.02 (0.34), residues: 257 sheet: 0.74 (0.40), residues: 162 loop : -1.29 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.008 0.002 HIS K 230 PHE 0.012 0.002 PHE K 240 TYR 0.012 0.002 TYR O 75 ARG 0.008 0.001 ARG L 21 *********************** 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 205 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 2.917 Fit side-chains revert: symmetry clash REVERT: K 145 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8728 (mt-10) REVERT: K 182 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8886 (ttt90) REVERT: M 144 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8003 (mt-10) REVERT: M 155 GLU cc_start: 0.7736 (pm20) cc_final: 0.7485 (pm20) REVERT: M 166 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8524 (mtpp) REVERT: N 1 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6776 (tmm) REVERT: N 28 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8045 (tp30) outliers start: 27 outliers final: 11 residues processed: 191 average time/residue: 3.2194 time to fit residues: 762.9183 Evaluate side-chains 178 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain P residue 108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 342 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 360 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN M 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 81962 Z= 0.296 Angle : 0.736 84.157 125857 Z= 0.380 Chirality : 0.042 1.064 16461 Planarity : 0.007 0.136 4639 Dihedral : 22.581 175.764 48434 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 2.44 % Allowed : 21.97 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.73 (0.23), residues: 1163 helix: 1.10 (0.34), residues: 256 sheet: 0.57 (0.38), residues: 177 loop : -1.43 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.015 0.001 PHE K 240 TYR 0.011 0.001 TYR O 75 ARG 0.006 0.000 ARG L 21 *********************** 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 189 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 3.216 Fit side-chains REVERT: K 145 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8731 (mt-10) REVERT: K 182 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8872 (ttt90) REVERT: N 1 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6768 (tmm) outliers start: 23 outliers final: 14 residues processed: 181 average time/residue: 3.2721 time to fit residues: 738.6449 Evaluate side-chains 190 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 6.9990 chunk 361 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 333 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 210 optimal weight: 50.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 136 GLN M 195 GLN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 81962 Z= 0.323 Angle : 0.729 84.032 125857 Z= 0.374 Chirality : 0.042 1.107 16461 Planarity : 0.007 0.137 4639 Dihedral : 22.585 175.654 48434 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 2.97 % Allowed : 20.91 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.23), residues: 1163 helix: 1.22 (0.35), residues: 250 sheet: 0.56 (0.38), residues: 177 loop : -1.41 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.013 0.001 PHE K 240 TYR 0.011 0.001 TYR O 75 ARG 0.006 0.001 ARG L 21 *********************** 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 214 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 3.004 Fit side-chains REVERT: K 145 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8740 (mt-10) REVERT: K 182 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8864 (ttt90) REVERT: N 1 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6772 (tmm) outliers start: 28 outliers final: 16 residues processed: 202 average time/residue: 3.2932 time to fit residues: 827.6883 Evaluate side-chains 192 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 28 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN M 195 GLN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 81962 Z= 0.322 Angle : 0.737 83.989 125857 Z= 0.380 Chirality : 0.043 1.091 16461 Planarity : 0.007 0.138 4639 Dihedral : 22.607 175.777 48434 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.90 % Rotamer: Outliers : 2.44 % Allowed : 21.76 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.65 (0.23), residues: 1163 helix: 1.25 (0.35), residues: 250 sheet: 0.60 (0.38), residues: 177 loop : -1.39 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.015 0.001 PHE K 240 TYR 0.011 0.001 TYR O 75 ARG 0.006 0.001 ARG L 48 *********************** 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 194 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 3.264 Fit side-chains REVERT: K 145 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8757 (mt-10) REVERT: K 182 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8854 (ttt90) REVERT: M 105 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8805 (mp) REVERT: N 1 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6687 (tmm) outliers start: 23 outliers final: 16 residues processed: 185 average time/residue: 3.3220 time to fit residues: 763.1397 Evaluate side-chains 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 27 ARG Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 314 optimal weight: 0.6980 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN M 195 GLN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 81962 Z= 0.297 Angle : 0.728 84.159 125857 Z= 0.375 Chirality : 0.042 1.074 16461 Planarity : 0.007 0.137 4639 Dihedral : 22.604 175.707 48434 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.55 % Allowed : 21.23 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.63 (0.23), residues: 1163 helix: 1.29 (0.35), residues: 250 sheet: 0.60 (0.38), residues: 177 loop : -1.38 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.015 0.001 PHE K 240 TYR 0.011 0.001 TYR O 75 ARG 0.009 0.001 ARG L 48 *********************** 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 195 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 3.217 Fit side-chains revert: symmetry clash REVERT: K 145 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8731 (mt-10) REVERT: K 182 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8851 (ttt90) REVERT: M 105 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8797 (mp) REVERT: N 1 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6684 (tmm) outliers start: 24 outliers final: 18 residues processed: 185 average time/residue: 3.3642 time to fit residues: 776.7024 Evaluate side-chains 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 27 ARG Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 28 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 0.0570 chunk 383 optimal weight: 8.9990 chunk 349 optimal weight: 4.9990 chunk 372 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 352 optimal weight: 8.9990 chunk 371 optimal weight: 1.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN M 195 GLN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 81962 Z= 0.223 Angle : 0.705 84.080 125857 Z= 0.367 Chirality : 0.040 1.071 16461 Planarity : 0.007 0.136 4639 Dihedral : 22.607 175.621 48434 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.34 % Allowed : 21.44 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.62 (0.23), residues: 1163 helix: 1.32 (0.35), residues: 250 sheet: 0.59 (0.38), residues: 177 loop : -1.37 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR O 75 ARG 0.003 0.000 ARG L 21 *********************** 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 192 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 3.222 Fit side-chains revert: symmetry clash REVERT: K 145 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8733 (mt-10) REVERT: K 182 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8846 (ttt90) REVERT: M 105 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8803 (mp) REVERT: N 1 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6681 (tmm) outliers start: 22 outliers final: 18 residues processed: 183 average time/residue: 3.3242 time to fit residues: 753.3506 Evaluate side-chains 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 27 ARG Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 5.9990 chunk 394 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 413 optimal weight: 0.0370 chunk 380 optimal weight: 0.2980 chunk 329 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 overall best weight: 3.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN M 195 GLN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 81962 Z= 0.224 Angle : 0.706 84.003 125857 Z= 0.366 Chirality : 0.040 1.074 16461 Planarity : 0.007 0.135 4639 Dihedral : 22.605 175.611 48434 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.23 % Allowed : 21.34 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.62 (0.23), residues: 1163 helix: 1.32 (0.35), residues: 250 sheet: 0.58 (0.38), residues: 177 loop : -1.37 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR O 75 ARG 0.004 0.000 ARG L 48 ********************** 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 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 3.263 Fit side-chains revert: symmetry clash REVERT: K 145 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8732 (mt-10) REVERT: K 182 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8848 (ttt90) REVERT: M 105 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8799 (mp) REVERT: N 1 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6681 (tmm) outliers start: 21 outliers final: 16 residues processed: 182 average time/residue: 3.2794 time to fit residues: 740.9038 Evaluate side-chains 188 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 6.9990 chunk 350 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 329 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 338 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN M 195 GLN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.056231 restraints weight = 353830.532| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 0.62 r_work: 0.2416 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2345 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 81962 Z= 0.282 Angle : 0.713 84.054 125857 Z= 0.367 Chirality : 0.041 1.093 16461 Planarity : 0.007 0.136 4639 Dihedral : 22.591 175.443 48434 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 2.23 % Allowed : 21.23 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.60 (0.23), residues: 1163 helix: 1.33 (0.35), residues: 250 sheet: 0.58 (0.38), residues: 177 loop : -1.35 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.016 0.001 PHE K 240 TYR 0.011 0.001 TYR O 75 ARG 0.006 0.000 ARG P 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36164.08 seconds wall clock time: 620 minutes 28.67 seconds (37228.67 seconds total)