Starting phenix.real_space_refine on Thu Feb 15 09:00:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e46_27881/02_2024/8e46_27881_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e46_27881/02_2024/8e46_27881.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e46_27881/02_2024/8e46_27881_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/8e46_27881/02_2024/8e46_27881_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e46_27881/02_2024/8e46_27881_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e46_27881/02_2024/8e46_27881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e46_27881/02_2024/8e46_27881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e46_27881/02_2024/8e46_27881_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e46_27881/02_2024/8e46_27881_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= -0.007 sd= 0.601 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: 6 Type Number sf(0) Gaussians P 3015 5.49 5 S 28 5.16 5 C 34623 2.51 5 N 13684 2.21 5 O 22595 1.98 5 H 41809 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 66": "OD1" <-> "OD2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K ASP 98": "OD1" <-> "OD2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 145": "OE1" <-> "OE2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ASP 187": "OD1" <-> "OD2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M ASP 154": "OD1" <-> "OD2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "M GLU 197": "OE1" <-> "OE2" Residue "M GLU 198": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O GLU 31": "OE1" <-> "OE2" Residue "O ASP 52": "OD1" <-> "OD2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "P ASP 22": "OD1" <-> "OD2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ASP 94": "OD1" <-> "OD2" Residue "Q ASP 31": "OD1" <-> "OD2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "Q TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 115754 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 93265 Classifications: {'RNA': 2897} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 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: 150 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 75 Unusual residues: {'UHP': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 75 Unusual residues: {'UHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AUHP I3001 " occ=0.50 ... (148 atoms not shown) pdb=" O9 BUHP I3001 " occ=0.50 Time building chain proxies: 38.81, per 1000 atoms: 0.34 Number of scatterers: 115754 At special positions: 0 Unit cell: (232.05, 224.175, 191.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 3015 15.00 O 22595 8.00 N 13684 7.00 C 34623 6.00 H 41809 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 75.90 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: 34 helices and 15 sheets defined 29.1% alpha, 17.2% beta 786 base pairs and 1620 stacking pairs defined. Time for finding SS restraints: 51.46 Creating SS restraints... Processing helix chain 'K' and resid 12 through 17 removed outlier: 5.252A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.225A 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: 4.043A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.756A 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: 3.580A 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: 3.897A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.034A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.393A 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: 3.689A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) 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: 7.187A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.332A 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: 3.822A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.176A 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: 3.559A 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: 3.558A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 3.874A 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: 3.597A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.650A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.517A pdb=" N LEU M 180 " --> pdb=" O ASP M 176 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.740A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.753A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.548A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.344A 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: 4.038A 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: 4.287A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.889A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.623A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 removed outlier: 3.505A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR P 38 " --> pdb=" O ASP P 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR P 39 " --> pdb=" O ILE P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.833A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.918A 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: 4.593A 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: 3.705A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.229A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.176A 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: 4.084A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'M' and resid 1 through 6 removed outlier: 5.012A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 4.969A 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 removed outlier: 6.991A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.711A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.299A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.152A 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: 3.728A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 3.588A 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: 3.539A pdb=" N LEU N 84 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 105 through 108 removed outlier: 6.110A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'O' and resid 52 through 57 removed outlier: 5.290A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 74 through 78 removed outlier: 7.010A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'P' and resid 2 through 8 removed outlier: 7.027A pdb=" N VAL P 106 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'P' and resid 73 through 79 removed outlier: 3.511A pdb=" N LYS P 73 " --> pdb=" O VAL P 106 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR P 100 " --> pdb=" O GLY P 79 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.534A pdb=" N SER Q 29 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS Q 37 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASP Q 31 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1885 hydrogen bonds 2952 hydrogen bond angles 0 basepair planarities 786 basepair parallelities 1620 stacking parallelities Total time for adding SS restraints: 129.42 Time building geometry restraints manager: 80.01 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: 41807 1.03 - 1.23: 631 1.23 - 1.42: 43187 1.42 - 1.62: 37971 1.62 - 1.81: 54 Bond restraints: 123650 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+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 1.80e+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 123645 not shown) Histogram of bond angle deviations from ideal: 74.44 - 86.55: 3 86.55 - 98.66: 0 98.66 - 110.77: 112079 110.77 - 122.88: 88493 122.88 - 135.00: 20841 Bond angle restraints: 221416 Sorted by residual: angle pdb=" C5' G I2061 " pdb=" C4' G I2061 " pdb=" H4' G I2061 " ideal model delta sigma weight residual 109.00 74.44 34.56 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C1' G7M I2069 " pdb=" N9 G7M I2069 " pdb=" C8 G7M I2069 " ideal model delta sigma weight residual 94.96 128.82 -33.86 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C3' G I2061 " pdb=" C4' G I2061 " pdb=" H4' G I2061 " ideal model delta sigma weight residual 109.00 78.93 30.07 3.00e+00 1.11e-01 1.00e+02 angle pdb=" O4' G I2061 " pdb=" C4' G I2061 " pdb=" H4' G I2061 " ideal model delta sigma weight residual 109.00 81.65 27.35 3.00e+00 1.11e-01 8.31e+01 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 125.87 -19.55 3.00e+00 1.11e-01 4.25e+01 ... (remaining 221411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 54784 35.96 - 71.91: 6627 71.91 - 107.87: 783 107.87 - 143.82: 16 143.82 - 179.78: 20 Dihedral angle restraints: 62230 sinusoidal: 58580 harmonic: 3650 Sorted by residual: dihedral pdb=" CA THR N 151 " pdb=" C THR N 151 " pdb=" N PRO N 152 " pdb=" CA PRO N 152 " ideal model delta harmonic sigma weight residual 180.00 -137.90 -42.10 0 5.00e+00 4.00e-02 7.09e+01 dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.78 -179.78 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 48.48 -176.48 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 62227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.092: 16446 1.092 - 2.185: 0 2.185 - 3.277: 0 3.277 - 4.370: 0 4.370 - 5.462: 4 Chirality restraints: 16450 Sorted by residual: chirality pdb=" C24AUHP I3001 " pdb=" C22AUHP I3001 " pdb=" C34AUHP I3001 " pdb=" C41AUHP I3001 " both_signs ideal model delta sigma weight residual False 2.79 -2.67 5.46 2.00e-01 2.50e+01 7.46e+02 chirality pdb=" C24BUHP I3001 " pdb=" C22BUHP I3001 " pdb=" C34BUHP I3001 " pdb=" C41BUHP I3001 " both_signs ideal model delta sigma weight residual False 2.79 -2.66 5.45 2.00e-01 2.50e+01 7.43e+02 chirality pdb=" C26AUHP I3001 " pdb=" C25AUHP I3001 " pdb=" C27AUHP I3001 " pdb=" O15AUHP I3001 " both_signs ideal model delta sigma weight residual False 2.56 -2.38 4.94 2.00e-01 2.50e+01 6.10e+02 ... (remaining 16447 not shown) Planarity restraints: 8160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.027 2.00e-02 2.50e+03 5.82e-01 7.63e+03 pdb=" C4' OMC I2498 " 0.440 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.687 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.568 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.215 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.900 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.222 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.899 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.029 2.00e-02 2.50e+03 5.73e-01 7.39e+03 pdb=" C4' 2MG I2445 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.646 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.566 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.211 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.902 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.227 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.876 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.037 2.00e-02 2.50e+03 5.66e-01 7.21e+03 pdb=" C4' OMG I2251 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.605 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.594 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.566 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.205 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.913 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.235 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.854 2.00e-02 2.50e+03 ... (remaining 8157 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 2373 2.08 - 2.71: 125539 2.71 - 3.34: 273174 3.34 - 3.97: 426149 3.97 - 4.60: 622128 Nonbonded interactions: 1449363 Sorted by model distance: nonbonded pdb=" O ASN O 128 " pdb="HD21 ASN O 128 " model vdw 1.453 1.850 nonbonded pdb=" H41 C I1838 " pdb=" OP2 A I1899 " model vdw 1.574 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.590 1.850 nonbonded pdb="HO2' G I1715 " pdb=" O6 G I1743 " model vdw 1.590 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.596 1.850 ... (remaining 1449358 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: 14.160 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: 0.890 Extract box with map and model: 64.940 Check model and map are aligned: 1.300 Set scattering table: 0.750 Process input model: 388.080 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 480.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.390 81841 Z= 0.341 Angle : 0.406 33.856 125653 Z= 0.196 Chirality : 0.085 5.462 16450 Planarity : 0.022 0.582 4633 Dihedral : 23.008 179.778 50568 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 0.53 % Allowed : 16.03 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.35 (0.25), residues: 1163 helix: 0.69 (0.35), residues: 241 sheet: 0.59 (0.40), residues: 180 loop : -0.77 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 60 HIS 0.002 0.000 HIS K 230 PHE 0.004 0.000 PHE K 240 TYR 0.006 0.001 TYR L 58 ARG 0.002 0.000 ARG L 69 *********************** 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 184 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 3.193 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 183 average time/residue: 3.2344 time to fit residues: 737.2477 Evaluate side-chains 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 186 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 107 optimal weight: 40.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 376 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 200 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 81841 Z= 0.293 Angle : 0.639 25.932 125653 Z= 0.335 Chirality : 0.043 1.973 16450 Planarity : 0.007 0.136 4633 Dihedral : 22.903 179.236 48335 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.64 % Favored : 95.18 % Rotamer: Outliers : 2.23 % Allowed : 15.29 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.43 (0.24), residues: 1163 helix: 0.87 (0.33), residues: 265 sheet: 0.55 (0.39), residues: 172 loop : -0.97 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 78 HIS 0.005 0.001 HIS K 200 PHE 0.009 0.001 PHE M 158 TYR 0.010 0.001 TYR K 103 ARG 0.004 0.000 ARG K 214 *********************** 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 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 3.123 Fit side-chains revert: symmetry clash REVERT: N 59 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8912 (ttt180) REVERT: O 95 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7517 (mtp-110) outliers start: 21 outliers final: 9 residues processed: 200 average time/residue: 3.2929 time to fit residues: 822.8909 Evaluate side-chains 176 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 36 GLU 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: 5.9990 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 5.9990 chunk 407 optimal weight: 5.9990 chunk 336 optimal weight: 5.9990 chunk 374 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 302 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 81841 Z= 0.376 Angle : 0.669 26.477 125653 Z= 0.355 Chirality : 0.045 1.800 16450 Planarity : 0.007 0.141 4633 Dihedral : 22.974 178.966 48332 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.50 % Favored : 94.24 % Rotamer: Outliers : 2.02 % Allowed : 15.29 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.58 (0.24), residues: 1163 helix: 1.03 (0.34), residues: 261 sheet: 0.19 (0.38), residues: 182 loop : -1.12 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.012 0.001 PHE N 118 TYR 0.009 0.001 TYR P 38 ARG 0.004 0.000 ARG R 3 *********************** 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 187 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 3.135 Fit side-chains revert: symmetry clash REVERT: K 181 MET cc_start: 0.9095 (mmt) cc_final: 0.8780 (mmt) REVERT: M 198 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: O 1 MET cc_start: 0.7210 (pp-130) cc_final: 0.6642 (pp-130) REVERT: O 95 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7488 (mtp-110) outliers start: 19 outliers final: 12 residues processed: 180 average time/residue: 3.5614 time to fit residues: 807.7490 Evaluate side-chains 168 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 36 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 108 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 81841 Z= 0.343 Angle : 0.649 26.045 125653 Z= 0.346 Chirality : 0.044 1.772 16450 Planarity : 0.007 0.137 4633 Dihedral : 22.984 179.839 48331 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Rotamer: Outliers : 1.91 % Allowed : 15.82 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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 (0.24), residues: 1163 helix: 1.10 (0.34), residues: 261 sheet: 0.06 (0.37), residues: 188 loop : -1.14 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.010 0.002 TYR P 38 ARG 0.004 0.000 ARG L 78 *********************** 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 170 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 3.146 Fit side-chains revert: symmetry clash REVERT: O 1 MET cc_start: 0.7225 (pp-130) cc_final: 0.6652 (pp-130) REVERT: O 95 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7471 (mtp-110) outliers start: 18 outliers final: 7 residues processed: 165 average time/residue: 3.5084 time to fit residues: 722.1438 Evaluate side-chains 166 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 29 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 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: 4.9990 chunk 360 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN N 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 81841 Z= 0.247 Angle : 0.624 26.026 125653 Z= 0.338 Chirality : 0.041 1.776 16450 Planarity : 0.007 0.134 4633 Dihedral : 22.995 179.690 48331 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 1.38 % Allowed : 16.03 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.53 (0.24), residues: 1163 helix: 1.18 (0.34), residues: 261 sheet: 0.20 (0.38), residues: 182 loop : -1.13 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.002 0.000 ARG R 3 *********************** 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 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 3.168 Fit side-chains revert: symmetry clash REVERT: O 1 MET cc_start: 0.7206 (pp-130) cc_final: 0.6625 (pp-130) outliers start: 13 outliers final: 9 residues processed: 177 average time/residue: 3.4595 time to fit residues: 763.7098 Evaluate side-chains 168 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 30 SER 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: 7.9990 chunk 79 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 333 optimal weight: 0.0570 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 210 optimal weight: 50.0000 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 81841 Z= 0.335 Angle : 0.654 26.053 125653 Z= 0.349 Chirality : 0.044 1.765 16450 Planarity : 0.007 0.138 4633 Dihedral : 23.006 179.830 48331 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.50 % Favored : 94.24 % Rotamer: Outliers : 1.80 % Allowed : 16.14 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.53 (0.24), residues: 1163 helix: 1.22 (0.34), residues: 261 sheet: 0.12 (0.38), residues: 182 loop : -1.12 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE N 118 TYR 0.009 0.002 TYR P 38 ARG 0.003 0.000 ARG K 214 *********************** 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 169 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 3.184 Fit side-chains revert: symmetry clash REVERT: M 2 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: O 95 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7476 (mtp-110) REVERT: P 95 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7356 (ttp-170) outliers start: 17 outliers final: 8 residues processed: 165 average time/residue: 3.4643 time to fit residues: 710.2315 Evaluate side-chains 178 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain P residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 chunk 399 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 81841 Z= 0.312 Angle : 0.645 26.012 125653 Z= 0.346 Chirality : 0.043 1.771 16450 Planarity : 0.007 0.137 4633 Dihedral : 23.002 179.806 48331 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.50 % Favored : 94.24 % Rotamer: Outliers : 1.59 % Allowed : 16.35 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.52 (0.24), residues: 1163 helix: 1.24 (0.34), residues: 261 sheet: 0.12 (0.38), residues: 182 loop : -1.12 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.003 0.000 ARG K 214 *********************** 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 183 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 2.972 Fit side-chains revert: symmetry clash REVERT: M 2 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: O 95 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7451 (mtp-110) REVERT: P 95 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7353 (ttp-170) outliers start: 15 outliers final: 9 residues processed: 176 average time/residue: 3.4209 time to fit residues: 746.3847 Evaluate side-chains 162 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain P residue 95 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 6.9990 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: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 81841 Z= 0.374 Angle : 0.672 25.950 125653 Z= 0.358 Chirality : 0.045 1.768 16450 Planarity : 0.007 0.139 4633 Dihedral : 23.039 179.339 48331 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 2.23 % Allowed : 15.92 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1163 helix: 1.21 (0.34), residues: 261 sheet: 0.07 (0.38), residues: 182 loop : -1.14 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.012 0.001 PHE K 240 TYR 0.010 0.002 TYR O 16 ARG 0.004 0.000 ARG K 214 *********************** 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 173 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 3.123 Fit side-chains revert: symmetry clash REVERT: M 2 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: O 95 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7454 (mtp-110) REVERT: P 95 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7356 (ttp-170) outliers start: 21 outliers final: 9 residues processed: 166 average time/residue: 3.3335 time to fit residues: 694.0783 Evaluate side-chains 169 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain P residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 4.9990 chunk 383 optimal weight: 4.9990 chunk 349 optimal weight: 1.9990 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: 6.9990 chunk 336 optimal weight: 0.9980 chunk 352 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 165 HIS N 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 81841 Z= 0.224 Angle : 0.634 26.109 125653 Z= 0.343 Chirality : 0.041 1.775 16450 Planarity : 0.007 0.135 4633 Dihedral : 23.045 179.992 48331 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.85 % Favored : 93.90 % Rotamer: Outliers : 1.80 % Allowed : 16.14 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1163 helix: 1.29 (0.34), residues: 261 sheet: 0.08 (0.38), residues: 182 loop : -1.11 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 78 HIS 0.004 0.001 HIS M 165 PHE 0.011 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.002 0.000 ARG L 78 *********************** 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 174 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 2.968 Fit side-chains revert: symmetry clash REVERT: M 2 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: O 95 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7444 (mtp-110) REVERT: P 95 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7348 (ttp-170) outliers start: 17 outliers final: 11 residues processed: 170 average time/residue: 3.3932 time to fit residues: 720.6055 Evaluate side-chains 163 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 5.9990 chunk 394 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 413 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 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: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 165 HIS N 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 81841 Z= 0.311 Angle : 0.643 26.024 125653 Z= 0.344 Chirality : 0.043 1.767 16450 Planarity : 0.007 0.136 4633 Dihedral : 23.021 179.469 48331 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.02 % Favored : 93.72 % Rotamer: Outliers : 1.49 % Allowed : 16.56 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1163 helix: 1.29 (0.34), residues: 261 sheet: 0.11 (0.38), residues: 182 loop : -1.10 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.005 0.001 HIS M 165 PHE 0.013 0.001 PHE K 240 TYR 0.009 0.002 TYR O 75 ARG 0.003 0.000 ARG K 214 ********************** 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 165 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 2.827 Fit side-chains revert: symmetry clash REVERT: M 2 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: O 95 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7444 (mtp-110) outliers start: 14 outliers final: 9 residues processed: 161 average time/residue: 3.3367 time to fit residues: 675.5737 Evaluate side-chains 160 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 30 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: 5.9990 chunk 100 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 338 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.063123 restraints weight = 268180.490| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 0.54 r_work: 0.2573 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 81841 Z= 0.298 Angle : 0.638 25.934 125653 Z= 0.343 Chirality : 0.043 1.772 16450 Planarity : 0.007 0.136 4633 Dihedral : 23.025 179.519 48331 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.93 % Favored : 93.81 % Rotamer: Outliers : 1.38 % Allowed : 16.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1163 helix: 1.30 (0.34), residues: 261 sheet: 0.11 (0.38), residues: 182 loop : -1.10 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.004 0.001 HIS K 200 PHE 0.013 0.001 PHE K 240 TYR 0.009 0.001 TYR O 75 ARG 0.003 0.000 ARG L 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33483.77 seconds wall clock time: 575 minutes 20.88 seconds (34520.88 seconds total)