Starting phenix.real_space_refine on Sat Dec 9 13:54:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/12_2023/8e48_27883_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/12_2023/8e48_27883.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/12_2023/8e48_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_27883/12_2023/8e48_27883_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/12_2023/8e48_27883_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/12_2023/8e48_27883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/12_2023/8e48_27883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/12_2023/8e48_27883_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e48_27883/12_2023/8e48_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-1.21rc1-5172/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: 65.52, 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: 68.53 Conformation dependent library (CDL) restraints added in 1.9 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: 57.48 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: 132.74 Time building geometry restraints manager: 73.08 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: 53139 35.38 - 70.75: 5144 70.75 - 106.13: 777 106.13 - 141.51: 5 141.51 - 176.89: 8 Dihedral angle restraints: 59073 sinusoidal: 55423 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 59070 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: 4.850 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: 29.950 Check model and map are aligned: 1.290 Set scattering table: 0.790 Process input model: 411.900 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.260 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:8.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 459.540 ------------------------------------------------------------------------------- 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 : 0.521 83.180 125857 Z= 0.233 Chirality : 0.029 1.047 16461 Planarity : 0.022 0.597 4639 Dihedral : 21.946 176.887 48286 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 : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 245 average time/residue: 3.3602 time to fit residues: 1020.1789 Evaluate side-chains 180 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 3.148 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8933 moved from start: 0.3610 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= 0.315 Angle : 0.762 83.945 125857 Z= 0.389 Chirality : 0.043 1.030 16461 Planarity : 0.007 0.145 4639 Dihedral : 21.763 176.132 46046 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.90 % Rotamer: Outliers : 2.97 % Allowed : 22.61 % Favored : 74.42 % 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: -0.16 (0.24), residues: 1163 helix: 1.19 (0.34), residues: 254 sheet: 0.82 (0.40), residues: 163 loop : -0.81 (0.21), residues: 746 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 0.011 0.002 TYR K 103 ARG 0.006 0.001 ARG L 21 *********************** 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 227 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 2.777 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 5 residues processed: 213 average time/residue: 3.1570 time to fit residues: 842.3073 Evaluate side-chains 183 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 3.184 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 1.2669 time to fit residues: 8.3720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 chunk 374 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- 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 O 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 81962 Z= 0.227 Angle : 0.670 83.527 125857 Z= 0.345 Chirality : 0.039 1.107 16461 Planarity : 0.006 0.134 4639 Dihedral : 21.751 176.600 46046 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.93 % Favored : 93.98 % Rotamer: Outliers : 2.76 % Allowed : 22.40 % Favored : 74.84 % 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: -0.25 (0.24), residues: 1163 helix: 1.26 (0.34), residues: 259 sheet: 0.84 (0.39), residues: 172 loop : -0.99 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS O 76 PHE 0.011 0.001 PHE K 240 TYR 0.010 0.001 TYR O 75 ARG 0.004 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 218 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 3.085 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 207 average time/residue: 3.2732 time to fit residues: 844.7633 Evaluate side-chains 185 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 3.056 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.9044 time to fit residues: 3.9864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 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: 0.9002 moved from start: 0.4700 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= 0.381 Angle : 0.773 84.092 125857 Z= 0.396 Chirality : 0.045 1.074 16461 Planarity : 0.007 0.141 4639 Dihedral : 21.804 176.257 46046 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.44 % Allowed : 22.61 % 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: -0.57 (0.23), residues: 1163 helix: 1.09 (0.34), residues: 257 sheet: 0.78 (0.39), residues: 172 loop : -1.28 (0.20), residues: 734 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 0.011 0.002 TYR O 75 ARG 0.007 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 192 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 3.089 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 181 average time/residue: 3.2320 time to fit residues: 732.4481 Evaluate side-chains 192 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 181 time to evaluate : 3.208 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 1.3108 time to fit residues: 8.6616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 3.9990 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: 1.9990 chunk 101 optimal weight: 6.9990 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.4723 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= 0.282 Angle : 0.727 84.155 125857 Z= 0.375 Chirality : 0.042 1.063 16461 Planarity : 0.007 0.135 4639 Dihedral : 21.813 175.821 46046 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.12 % Allowed : 23.04 % Favored : 74.84 % 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: 1.13 (0.34), residues: 256 sheet: 0.74 (0.39), residues: 170 loop : -1.33 (0.20), residues: 737 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 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR O 75 ARG 0.005 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 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 3.033 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 196 average time/residue: 3.2581 time to fit residues: 799.2428 Evaluate side-chains 192 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.9567 time to fit residues: 4.1368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 333 optimal weight: 0.4980 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: 5.2988 ------------------------------------------------------------------------------- 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: 0.4917 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= 0.319 Angle : 0.727 84.026 125857 Z= 0.374 Chirality : 0.042 1.102 16461 Planarity : 0.007 0.138 4639 Dihedral : 21.817 175.582 46046 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 2.44 % Allowed : 22.51 % Favored : 75.05 % 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: -0.56 (0.23), residues: 1163 helix: 1.26 (0.35), residues: 250 sheet: 0.75 (0.39), residues: 170 loop : -1.30 (0.20), residues: 743 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 0.013 0.001 PHE K 240 TYR 0.012 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 200 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 3.119 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 192 average time/residue: 3.3470 time to fit residues: 808.4944 Evaluate side-chains 189 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 1.6157 time to fit residues: 14.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5109 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= 0.321 Angle : 0.735 84.083 125857 Z= 0.379 Chirality : 0.043 1.086 16461 Planarity : 0.007 0.137 4639 Dihedral : 21.859 175.751 46046 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 2.55 % Allowed : 21.66 % 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: -0.60 (0.23), residues: 1163 helix: 1.25 (0.35), residues: 250 sheet: 0.62 (0.38), residues: 177 loop : -1.33 (0.20), residues: 736 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 0.016 0.001 PHE K 240 TYR 0.011 0.001 TYR O 75 ARG 0.005 0.000 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 200 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 3.141 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 189 average time/residue: 3.2563 time to fit residues: 770.3591 Evaluate side-chains 187 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 3.218 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.9284 time to fit residues: 7.5067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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 R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.5131 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= 0.303 Angle : 0.721 84.154 125857 Z= 0.372 Chirality : 0.042 1.091 16461 Planarity : 0.007 0.137 4639 Dihedral : 21.852 175.547 46046 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 1.91 % Allowed : 22.29 % 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: -0.57 (0.23), residues: 1163 helix: 1.30 (0.35), residues: 250 sheet: 0.64 (0.38), residues: 177 loop : -1.32 (0.21), 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 0.000 ARG L 21 *********************** 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 192 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 3.097 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 185 average time/residue: 3.3331 time to fit residues: 767.9181 Evaluate side-chains 187 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 1.3048 time to fit residues: 8.6059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 2.9990 chunk 383 optimal weight: 0.9990 chunk 349 optimal weight: 2.9990 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: 6.9990 chunk 352 optimal weight: 4.9990 chunk 371 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: 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: 0.8984 moved from start: 0.5133 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= 0.211 Angle : 0.697 84.060 125857 Z= 0.363 Chirality : 0.040 1.078 16461 Planarity : 0.007 0.135 4639 Dihedral : 21.855 175.481 46046 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 1.70 % Allowed : 22.40 % Favored : 75.90 % 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: -0.56 (0.23), residues: 1163 helix: 1.34 (0.35), residues: 250 sheet: 0.63 (0.38), residues: 177 loop : -1.32 (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 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR O 75 ARG 0.006 0.000 ARG L 48 *********************** 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 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 3.123 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 185 average time/residue: 3.2971 time to fit residues: 759.6187 Evaluate side-chains 187 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 1.3204 time to fit residues: 8.6927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 240 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 413 optimal weight: 5.9990 chunk 380 optimal weight: 0.6980 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: 4.7388 ------------------------------------------------------------------------------- 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: 0.8986 moved from start: 0.5193 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= 0.289 Angle : 0.709 83.841 125857 Z= 0.366 Chirality : 0.041 1.094 16461 Planarity : 0.007 0.136 4639 Dihedral : 21.843 175.550 46046 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 1.59 % Allowed : 22.40 % Favored : 76.01 % 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: 1.28 (0.35), residues: 250 sheet: 0.46 (0.37), residues: 180 loop : -1.32 (0.21), residues: 733 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 0.000 ARG L 21 ********************** 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 190 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 3.108 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 185 average time/residue: 3.3316 time to fit residues: 769.6097 Evaluate side-chains 186 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 3.208 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.9606 time to fit residues: 5.8786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 100 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 338 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.105203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.056530 restraints weight = 352714.154| |-----------------------------------------------------------------------------| r_work (start): 0.2520 rms_B_bonded: 0.61 r_work: 0.2418 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2347 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 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 = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.5199 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= 0.265 Angle : 0.703 84.007 125857 Z= 0.363 Chirality : 0.040 1.085 16461 Planarity : 0.007 0.135 4639 Dihedral : 21.842 175.521 46046 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.12 % Allowed : 21.97 % Favored : 75.90 % 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: -0.61 (0.23), residues: 1163 helix: 1.32 (0.35), residues: 250 sheet: 0.46 (0.38), residues: 180 loop : -1.32 (0.21), residues: 733 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 0.014 0.001 PHE K 240 TYR 0.011 0.001 TYR O 75 ARG 0.006 0.000 ARG L 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35265.42 seconds wall clock time: 603 minutes 58.87 seconds (36238.87 seconds total)