Starting phenix.real_space_refine on Fri Jan 19 20:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e47_27882/01_2024/8e47_27882_neut_trim_updated.pdb" } resolution = 2.32 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= -0.003 sd= 0.798 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 3022 5.49 5 S 29 5.16 5 C 34647 2.51 5 N 13710 2.21 5 O 22622 1.98 5 F 1 1.80 5 H 41886 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K GLU 199": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 99": "OE1" <-> "OE2" Residue "N GLU 183": "OE1" <-> "OE2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O GLU 31": "OE1" <-> "OE2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "P GLU 2": "OE1" <-> "OE2" Residue "P ASP 22": "OD1" <-> "OD2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ASP 94": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 115917 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93494 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 279, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1386, 'rna3p_pyr': 1061} 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': 279, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1386, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 436, 'rna3p': 2461} 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: 100550 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 84 Unusual residues: {'UH6': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" P A G I2061 " occ=0.63 ... (66 atoms not shown) pdb=" H22B G I2061 " occ=0.37 residue: pdb=" P A A I2062 " occ=0.63 ... (64 atoms not shown) pdb=" H2 B A I2062 " occ=0.37 residue: pdb=" P A C I2063 " occ=0.63 ... (60 atoms not shown) pdb=" H6 B C I2063 " occ=0.37 residue: pdb=" P A C I2601 " occ=0.59 ... (60 atoms not shown) pdb=" H6 B C I2601 " occ=0.41 residue: pdb=" P A A I2602 " occ=0.59 ... (64 atoms not shown) pdb=" H2 B A I2602 " occ=0.41 residue: pdb=" P A G I2603 " occ=0.59 ... (66 atoms not shown) pdb=" H22B G I2603 " occ=0.41 Time building chain proxies: 64.62, per 1000 atoms: 0.56 Number of scatterers: 115917 At special positions: 0 Unit cell: (232.75, 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 29 16.00 P 3022 15.00 F 1 9.00 O 22622 8.00 N 13710 7.00 C 34647 6.00 H 41886 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: 69.41 Conformation dependent library (CDL) restraints added in 2.1 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 35 helices and 12 sheets defined 29.9% alpha, 15.2% beta 539 base pairs and 1618 stacking pairs defined. Time for finding SS restraints: 53.80 Creating SS restraints... Processing helix chain 'K' and resid 10 through 17 removed outlier: 3.721A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 17' Processing helix chain 'K' and resid 30 through 35 removed outlier: 4.112A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.863A 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: 3.657A 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: 3.984A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.268A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.630A 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: 3.754A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.646A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.778A 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: 7.033A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.520A 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: 4.073A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.001A 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: 3.603A 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: 3.749A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 4.112A 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: 3.537A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.722A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.674A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 removed outlier: 3.754A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 72 removed outlier: 3.785A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.896A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.529A 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: 3.805A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.353A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU O 109 " --> pdb=" O VAL O 105 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 122 removed outlier: 3.630A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.718A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 40 removed outlier: 3.689A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR P 38 " --> pdb=" O ASP P 34 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR P 39 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.938A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 removed outlier: 3.742A pdb=" N LEU P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 5.848A 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: 4.986A 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: 4.239A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.810A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 162 through 165 removed outlier: 3.635A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.287A 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: 4.277A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'M' and resid 2 through 6 removed outlier: 4.396A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 44 through 47 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 removed outlier: 6.063A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL M 146 " --> pdb=" O LYS M 166 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR M 150 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.443A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU N 168 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.834A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.170A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'O' and resid 52 through 57 removed outlier: 5.061A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'O' and resid 74 through 78 removed outlier: 3.518A pdb=" N THR O 78 " --> pdb=" O GLY O 83 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'P' and resid 2 through 8 removed outlier: 4.731A pdb=" N THR P 100 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS P 73 " --> pdb=" O VAL P 106 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1251 hydrogen bonds 1854 hydrogen bond angles 0 basepair planarities 539 basepair parallelities 1621 stacking parallelities Total time for adding SS restraints: 122.61 Time building geometry restraints manager: 73.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 41884 1.04 - 1.23: 1454 1.23 - 1.43: 44191 1.43 - 1.63: 36248 1.63 - 1.82: 56 Bond restraints: 123833 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.413 0.389 2.00e-02 2.50e+03 3.79e+02 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=" 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 1.79e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.370 0.265 2.00e-02 2.50e+03 1.76e+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 9.49e+01 ... (remaining 123828 not shown) Histogram of bond angle deviations from ideal: 68.87 - 82.08: 21 82.08 - 95.29: 0 95.29 - 108.51: 38980 108.51 - 121.72: 158436 121.72 - 134.93: 24331 Bond angle restraints: 221768 Sorted by residual: angle pdb=" O3' A I 752 " pdb=" C3' A I 752 " pdb=" H3' A I 752 " ideal model delta sigma weight residual 109.00 68.87 40.13 3.00e+00 1.11e-01 1.79e+02 angle pdb=" O3'A A I2062 " pdb=" C3'A A I2062 " pdb=" H3'A A I2062 " ideal model delta sigma weight residual 109.00 69.16 39.84 3.00e+00 1.11e-01 1.76e+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 73.86 35.14 3.00e+00 1.11e-01 1.37e+02 angle pdb=" O3' G I2508 " pdb=" C3' G I2508 " pdb=" H3' G I2508 " ideal model delta sigma weight residual 109.00 74.52 34.48 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C5'B A I2062 " pdb=" C4'B A I2062 " pdb=" H4'B A I2062 " ideal model delta sigma weight residual 109.00 74.60 34.40 3.00e+00 1.11e-01 1.31e+02 ... (remaining 221763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 53246 35.92 - 71.84: 5072 71.84 - 107.77: 768 107.77 - 143.69: 7 143.69 - 179.61: 10 Dihedral angle restraints: 59103 sinusoidal: 55453 harmonic: 3650 Sorted by residual: 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 49.79 -177.79 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 58.27 173.73 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 40.14 -168.14 1 1.70e+01 3.46e-03 6.57e+01 ... (remaining 59100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.094: 16459 1.094 - 2.188: 0 2.188 - 3.282: 0 3.282 - 4.376: 0 4.376 - 5.470: 5 Chirality restraints: 16464 Sorted by residual: chirality pdb=" C37 UH6 I3001 " pdb=" C36 UH6 I3001 " pdb=" C38 UH6 I3001 " pdb=" C42 UH6 I3001 " both_signs ideal model delta sigma weight residual False 2.68 -2.79 5.47 2.00e-01 2.50e+01 7.48e+02 chirality pdb=" C53 UH6 I3001 " pdb=" C15 UH6 I3001 " pdb=" C52 UH6 I3001 " pdb=" C54 UH6 I3001 " both_signs ideal model delta sigma weight residual False -2.79 2.61 -5.40 2.00e-01 2.50e+01 7.30e+02 chirality pdb=" C35 UH6 I3001 " pdb=" C18 UH6 I3001 " pdb=" C50 UH6 I3001 " pdb=" O15 UH6 I3001 " both_signs ideal model delta sigma weight residual False -2.57 2.63 -5.20 2.00e-01 2.50e+01 6.76e+02 ... (remaining 16461 not shown) Planarity restraints: 8171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.031 2.00e-02 2.50e+03 5.96e-01 8.00e+03 pdb=" C4' OMC I2498 " 0.451 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.737 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.579 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.222 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.898 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.208 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.932 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 5.67e-01 7.25e+03 pdb=" C4' 2MG I2445 " -0.430 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.604 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.571 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.915 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.234 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.856 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.041 2.00e-02 2.50e+03 5.64e-01 7.15e+03 pdb=" C4' OMG I2251 " 0.425 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.592 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.567 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.204 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.916 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.236 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.845 2.00e-02 2.50e+03 ... (remaining 8168 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 6229 2.21 - 2.81: 154233 2.81 - 3.40: 257672 3.40 - 4.00: 410069 4.00 - 4.60: 582916 Nonbonded interactions: 1411119 Sorted by model distance: nonbonded pdb=" H41 C I1838 " pdb=" OP2 A I1899 " model vdw 1.611 1.850 nonbonded pdb=" O4 U J 65 " pdb="HO2' A J 108 " model vdw 1.649 1.850 nonbonded pdb="HO2' G I 141 " pdb=" O4' A I 142 " model vdw 1.654 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.658 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.661 1.850 ... (remaining 1411114 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=0.00 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: 8.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.850 Extract box with map and model: 30.080 Check model and map are aligned: 1.250 Set scattering table: 0.780 Process input model: 400.560 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 454.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 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 81947 Z= 0.315 Angle : 0.422 33.748 125830 Z= 0.204 Chirality : 0.094 5.470 16464 Planarity : 0.022 0.596 4637 Dihedral : 21.983 179.611 48265 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.96 % Allowed : 21.55 % Favored : 77.49 % 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: 0.60 (0.25), residues: 1163 helix: 1.71 (0.36), residues: 238 sheet: 1.15 (0.37), residues: 210 loop : -0.27 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 K 83 ARG 0.011 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 181 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 3.018 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 180 average time/residue: 3.2145 time to fit residues: 721.7644 Evaluate side-chains 174 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 52 ASP Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 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: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 9 GLN N 42 ASN P 31 GLN P 61 ASN R 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 81947 Z= 0.252 Angle : 0.639 28.648 125830 Z= 0.345 Chirality : 0.045 1.897 16464 Planarity : 0.007 0.134 4637 Dihedral : 21.795 177.699 46036 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.23 % Allowed : 19.75 % Favored : 78.03 % 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: 0.08 (0.24), residues: 1163 helix: 1.37 (0.34), residues: 256 sheet: 0.92 (0.38), residues: 186 loop : -0.69 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.007 0.001 HIS K 230 PHE 0.008 0.001 PHE N 127 TYR 0.011 0.001 TYR K 103 ARG 0.004 0.001 ARG L 60 *********************** 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 194 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 3.064 Fit side-chains REVERT: K 97 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8722 (mmtm) REVERT: N 1 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.5983 (tmm) REVERT: N 74 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7740 (mp0) outliers start: 21 outliers final: 7 residues processed: 185 average time/residue: 3.1742 time to fit residues: 735.2662 Evaluate side-chains 180 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 131 ASN 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: 1.9990 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 2.9990 chunk 407 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 374 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN N 42 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 81947 Z= 0.222 Angle : 0.606 26.631 125830 Z= 0.329 Chirality : 0.045 1.946 16464 Planarity : 0.006 0.133 4637 Dihedral : 21.808 178.325 46027 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 1.80 % Allowed : 19.75 % Favored : 78.45 % 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: -0.15 (0.24), residues: 1163 helix: 1.30 (0.33), residues: 261 sheet: 0.63 (0.39), residues: 170 loop : -0.82 (0.21), residues: 732 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 0.012 0.001 PHE K 240 TYR 0.010 0.001 TYR K 103 ARG 0.005 0.000 ARG M 170 *********************** 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 188 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 3.085 Fit side-chains REVERT: M 149 ILE cc_start: 0.8848 (pt) cc_final: 0.8475 (mt) REVERT: N 74 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: O 142 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7577 (mp) outliers start: 17 outliers final: 8 residues processed: 181 average time/residue: 3.2329 time to fit residues: 736.1202 Evaluate side-chains 177 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 0.0870 chunk 283 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 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: 0.5980 chunk 197 optimal weight: 5.9990 chunk 359 optimal weight: 8.9990 chunk 108 optimal weight: 50.0000 overall best weight: 4.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 115 GLN N 42 ASN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 81947 Z= 0.256 Angle : 0.644 26.771 125830 Z= 0.349 Chirality : 0.046 1.908 16464 Planarity : 0.007 0.134 4637 Dihedral : 21.828 177.741 46027 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.50 % Rotamer: Outliers : 2.12 % Allowed : 18.90 % Favored : 78.98 % 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: -0.31 (0.24), residues: 1163 helix: 1.19 (0.33), residues: 261 sheet: 0.60 (0.39), residues: 170 loop : -0.97 (0.21), residues: 732 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 0.010 0.001 TYR O 75 ARG 0.006 0.000 ARG P 95 *********************** 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 187 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 136 GLN cc_start: 0.9241 (tp40) cc_final: 0.8993 (tp40) REVERT: M 149 ILE cc_start: 0.8852 (pt) cc_final: 0.8554 (mt) REVERT: N 74 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: N 201 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8512 (pp) REVERT: O 142 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7639 (mp) outliers start: 20 outliers final: 10 residues processed: 179 average time/residue: 3.1884 time to fit residues: 712.3455 Evaluate side-chains 181 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 24 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN N 42 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 81947 Z= 0.301 Angle : 0.660 25.757 125830 Z= 0.355 Chirality : 0.047 1.931 16464 Planarity : 0.007 0.137 4637 Dihedral : 21.871 177.995 46027 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 2.44 % Allowed : 18.47 % Favored : 79.09 % 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: -0.51 (0.23), residues: 1163 helix: 1.16 (0.33), residues: 255 sheet: 0.40 (0.38), residues: 176 loop : -1.12 (0.21), residues: 732 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 0.010 0.001 TYR O 75 ARG 0.007 0.001 ARG P 95 *********************** 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 : 3.045 Fit side-chains REVERT: M 136 GLN cc_start: 0.9251 (tp40) cc_final: 0.8994 (tp40) REVERT: M 149 ILE cc_start: 0.8849 (pt) cc_final: 0.8614 (mt) REVERT: N 74 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: N 201 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8536 (pp) outliers start: 23 outliers final: 9 residues processed: 180 average time/residue: 3.1375 time to fit residues: 710.9741 Evaluate side-chains 180 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain Q residue 46 ASP 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: 5.9990 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: 3.9990 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 210 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 81947 Z= 0.337 Angle : 0.689 26.144 125830 Z= 0.369 Chirality : 0.048 1.961 16464 Planarity : 0.007 0.137 4637 Dihedral : 21.906 178.223 46027 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 2.55 % Allowed : 18.37 % Favored : 79.09 % 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: 1.09 (0.33), residues: 255 sheet: 0.26 (0.38), residues: 176 loop : -1.18 (0.21), residues: 732 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 0.016 0.001 PHE K 240 TYR 0.011 0.001 TYR O 75 ARG 0.007 0.000 ARG P 95 *********************** 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 197 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 21 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8165 (mtm180) REVERT: M 122 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7968 (tm-30) REVERT: M 136 GLN cc_start: 0.9261 (tp40) cc_final: 0.9003 (tp40) REVERT: M 149 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8630 (mt) REVERT: M 194 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.7991 (mptt) REVERT: M 198 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: N 74 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: N 201 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8525 (pp) outliers start: 24 outliers final: 12 residues processed: 187 average time/residue: 3.0620 time to fit residues: 721.3956 Evaluate side-chains 181 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain Q residue 46 ASP 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: 5.9990 chunk 228 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 338 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 115 GLN N 185 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 81947 Z= 0.264 Angle : 0.657 25.957 125830 Z= 0.355 Chirality : 0.046 1.918 16464 Planarity : 0.007 0.135 4637 Dihedral : 21.906 177.911 46027 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 2.12 % Allowed : 18.68 % Favored : 79.19 % 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: 1.11 (0.33), residues: 255 sheet: 0.28 (0.39), residues: 176 loop : -1.23 (0.21), residues: 732 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 0.010 0.001 TYR O 75 ARG 0.009 0.000 ARG P 95 *********************** 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 186 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 3.047 Fit side-chains REVERT: M 1 MET cc_start: 0.8200 (ptm) cc_final: 0.7987 (ptm) REVERT: M 122 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8009 (tm-30) REVERT: M 136 GLN cc_start: 0.9258 (tp40) cc_final: 0.8995 (tp40) REVERT: M 149 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8639 (mt) REVERT: N 74 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: N 201 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8528 (pp) outliers start: 20 outliers final: 12 residues processed: 178 average time/residue: 3.2417 time to fit residues: 729.1786 Evaluate side-chains 186 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain Q residue 46 ASP 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: 7.9990 chunk 314 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 115 GLN P 31 GLN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 81947 Z= 0.313 Angle : 0.667 25.869 125830 Z= 0.358 Chirality : 0.047 1.903 16464 Planarity : 0.007 0.137 4637 Dihedral : 21.900 178.173 46027 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 2.34 % Allowed : 18.47 % Favored : 79.19 % 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: 1.11 (0.33), residues: 255 sheet: 0.33 (0.39), residues: 175 loop : -1.25 (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 0.010 0.001 TYR O 75 ARG 0.009 0.001 ARG P 95 *********************** 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 194 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 3.045 Fit side-chains REVERT: M 1 MET cc_start: 0.8220 (ptm) cc_final: 0.8013 (ptm) REVERT: M 122 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7968 (tm-30) REVERT: M 136 GLN cc_start: 0.9270 (tp40) cc_final: 0.9008 (tp40) REVERT: M 198 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: N 74 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: N 201 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8548 (pp) REVERT: P 42 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9199 (tttt) outliers start: 22 outliers final: 12 residues processed: 187 average time/residue: 3.1406 time to fit residues: 733.3698 Evaluate side-chains 181 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain R residue 45 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 4.9990 chunk 383 optimal weight: 6.9990 chunk 349 optimal weight: 2.9990 chunk 372 optimal weight: 4.9990 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: 3.9990 chunk 352 optimal weight: 7.9990 chunk 371 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 115 GLN P 31 GLN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 81947 Z= 0.267 Angle : 0.653 25.685 125830 Z= 0.354 Chirality : 0.046 1.905 16464 Planarity : 0.007 0.136 4637 Dihedral : 21.900 178.115 46027 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 2.12 % Allowed : 18.68 % Favored : 79.19 % 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: 1.00 (0.33), residues: 261 sheet: 0.47 (0.39), residues: 168 loop : -1.22 (0.21), residues: 734 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 0.009 0.000 ARG P 95 *********************** 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 185 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 3.046 Fit side-chains REVERT: M 1 MET cc_start: 0.8252 (ptm) cc_final: 0.7977 (ptm) REVERT: M 122 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7970 (tm-30) REVERT: M 136 GLN cc_start: 0.9270 (tp40) cc_final: 0.9008 (tp40) REVERT: N 1 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6614 (ttm) REVERT: N 74 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: N 201 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8545 (pp) REVERT: P 42 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9210 (tttt) outliers start: 20 outliers final: 13 residues processed: 178 average time/residue: 3.2004 time to fit residues: 711.6171 Evaluate side-chains 187 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain R residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 4.9990 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: 4.9990 chunk 380 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 115 GLN M 156 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 81947 Z= 0.265 Angle : 0.653 25.668 125830 Z= 0.353 Chirality : 0.046 1.905 16464 Planarity : 0.007 0.136 4637 Dihedral : 21.899 178.113 46027 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 2.23 % Allowed : 18.68 % Favored : 79.09 % 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: 1.00 (0.33), residues: 261 sheet: 0.47 (0.39), residues: 168 loop : -1.22 (0.21), residues: 734 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 P 95 ********************** 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 : 3.110 Fit side-chains REVERT: M 1 MET cc_start: 0.8243 (ptm) cc_final: 0.7989 (ptm) REVERT: M 122 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7970 (tm-30) REVERT: M 136 GLN cc_start: 0.9270 (tp40) cc_final: 0.9008 (tp40) REVERT: M 194 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7886 (mptt) REVERT: M 198 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: N 1 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6602 (ttm) REVERT: N 74 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: N 201 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8545 (pp) REVERT: P 42 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9209 (tttt) outliers start: 21 outliers final: 12 residues processed: 182 average time/residue: 3.2719 time to fit residues: 744.9760 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain R residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 329 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 338 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 115 GLN P 31 GLN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.057298 restraints weight = 298033.503| |-----------------------------------------------------------------------------| r_work (start): 0.2517 rms_B_bonded: 0.59 r_work: 0.2415 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2344 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| r_final: 0.2350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 81947 Z= 0.212 Angle : 0.637 25.600 125830 Z= 0.348 Chirality : 0.045 1.908 16464 Planarity : 0.007 0.135 4637 Dihedral : 21.901 178.045 46027 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 2.02 % Allowed : 18.90 % Favored : 79.09 % 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: 1.15 (0.34), residues: 255 sheet: 0.35 (0.39), residues: 175 loop : -1.25 (0.21), residues: 733 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 0.010 0.001 TYR O 75 ARG 0.008 0.000 ARG P 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33326.89 seconds wall clock time: 572 minutes 21.27 seconds (34341.27 seconds total)