Starting phenix.real_space_refine on Tue Mar 12 17:07:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e36_27858/03_2024/8e36_27858_neut_trim_updated.pdb" } resolution = 2.38 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= -0.023 sd= 0.861 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 3015 5.49 5 S 28 5.16 5 C 34597 2.51 5 N 13686 2.21 5 O 22575 1.98 5 F 2 1.80 5 H 41809 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K ASP 187": "OD1" <-> "OD2" Residue "K ASP 229": "OD1" <-> "OD2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 181": "OD1" <-> "OD2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O GLU 31": "OE1" <-> "OE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ASP 49": "OD1" <-> "OD2" Residue "O ASP 52": "OD1" <-> "OD2" Residue "O TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 90": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ASP 62": "OD1" <-> "OD2" Residue "P ASP 65": "OD1" <-> "OD2" Residue "P ASP 77": "OD1" <-> "OD2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "Q TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 115712 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: 108 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 54 Unusual residues: {'UEC': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 54 Unusual residues: {'UEC': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AUEC I3001 " occ=0.50 ... (106 atoms not shown) pdb=" O7 BUEC I3001 " occ=0.50 Time building chain proxies: 38.81, per 1000 atoms: 0.34 Number of scatterers: 115712 At special positions: 0 Unit cell: (229.656, 222.221, 190.003, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 28 16.00 P 3015 15.00 F 2 9.00 O 22575 8.00 N 13686 7.00 C 34597 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 84.53 Conformation dependent library (CDL) restraints added in 2.9 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 35 helices and 15 sheets defined 30.3% alpha, 17.6% beta 914 base pairs and 1599 stacking pairs defined. Time for finding SS restraints: 59.05 Creating SS restraints... Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.539A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 16' Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.814A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.630A 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 Proline residue: K 136 - end of helix Processing helix chain 'K' and resid 197 through 203 removed outlier: 4.579A pdb=" N MET K 201 " --> pdb=" O ASN K 197 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG K 203 " --> pdb=" O GLU K 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 197 through 203' Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.827A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 6.983A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.323A 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 260 through 265 removed outlier: 6.947A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 265' Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.524A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.694A 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: 6.828A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.188A 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: 3.854A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.358A 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 Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 41 removed outlier: 3.607A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 165 removed outlier: 4.376A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU M 164 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N HIS M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 3.611A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 removed outlier: 3.586A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 72 removed outlier: 3.721A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.532A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.271A 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: 3.713A 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: 4.107A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 123 removed outlier: 3.885A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS O 123 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.998A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 removed outlier: 3.907A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.712A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.797A 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 25 removed outlier: 4.136A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.616A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE K 74 " --> pdb=" O SER K 118 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER K 118 " --> pdb=" O ILE K 74 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 162 through 165 removed outlier: 3.866A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.156A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L' and resid 120 through 123 Processing sheet with id= 6, first strand: chain 'M' and resid 1 through 6 removed outlier: 4.452A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'M' and resid 42 through 47 removed outlier: 7.659A pdb=" N GLY M 42 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ASP M 91 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'M' and resid 117 through 120 Processing sheet with id= 9, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.108A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.513A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'N' and resid 79 through 84 removed outlier: 5.692A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.643A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.954A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'O' and resid 74 through 78 removed outlier: 6.981A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'P' and resid 2 through 8 269 hydrogen bonds defined for protein. 789 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2294 hydrogen bonds 3636 hydrogen bond angles 0 basepair planarities 914 basepair parallelities 1599 stacking parallelities Total time for adding SS restraints: 136.21 Time building geometry restraints manager: 88.06 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: 634 1.23 - 1.42: 43745 1.42 - 1.62: 37368 1.62 - 1.81: 54 Bond restraints: 123608 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.81e+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 3.79e+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 1.369 0.266 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C15AUEC I3001 " pdb=" C16AUEC I3001 " ideal model delta sigma weight residual 1.590 1.350 0.240 2.00e-02 2.50e+03 1.45e+02 ... (remaining 123603 not shown) Histogram of bond angle deviations from ideal: 74.40 - 86.50: 3 86.50 - 98.60: 0 98.60 - 110.70: 111111 110.70 - 122.80: 89075 122.80 - 134.90: 21149 Bond angle restraints: 221338 Sorted by residual: angle pdb=" C4 AUEC I3001 " pdb=" C5 AUEC I3001 " pdb=" C6 AUEC I3001 " ideal model delta sigma weight residual 68.55 119.89 -51.34 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C4 BUEC I3001 " pdb=" C5 BUEC I3001 " pdb=" C6 BUEC I3001 " ideal model delta sigma weight residual 68.55 119.78 -51.23 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C3 AUEC I3001 " pdb=" C4 AUEC I3001 " pdb=" C5 AUEC I3001 " ideal model delta sigma weight residual 85.73 124.92 -39.19 3.00e+00 1.11e-01 1.71e+02 angle pdb=" C3 BUEC I3001 " pdb=" C4 BUEC I3001 " pdb=" C5 BUEC I3001 " ideal model delta sigma weight residual 85.73 124.84 -39.11 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C1 BUEC I3001 " pdb=" C15BUEC I3001 " pdb=" C16BUEC I3001 " ideal model delta sigma weight residual 85.75 122.05 -36.30 3.00e+00 1.11e-01 1.46e+02 ... (remaining 221333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 53856 35.36 - 70.72: 7485 70.72 - 106.08: 815 106.08 - 141.44: 39 141.44 - 176.80: 17 Dihedral angle restraints: 62212 sinusoidal: 58562 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 48.80 -176.80 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 41.73 -169.73 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' U I1313 " pdb=" C1' U I1313 " pdb=" N1 U I1313 " pdb=" C2 U I1313 " ideal model delta sinusoidal sigma weight residual 200.00 93.50 106.50 1 1.50e+01 4.44e-03 5.48e+01 ... (remaining 62209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 16259 0.079 - 0.159: 155 0.159 - 0.238: 1 0.238 - 0.317: 4 0.317 - 0.396: 1 Chirality restraints: 16420 Sorted by residual: chirality pdb=" CA LYS L 29 " pdb=" N LYS L 29 " pdb=" C LYS L 29 " pdb=" CB LYS L 29 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C17BUEC I3001 " pdb=" C16BUEC I3001 " pdb=" C18BUEC I3001 " pdb=" C29BUEC I3001 " both_signs ideal model delta sigma weight residual False -2.76 -2.44 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C17AUEC I3001 " pdb=" C16AUEC I3001 " pdb=" C18AUEC I3001 " pdb=" C29AUEC I3001 " both_signs ideal model delta sigma weight residual False -2.76 -2.46 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 16417 not shown) Planarity restraints: 8170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.030 2.00e-02 2.50e+03 6.01e-01 8.11e+03 pdb=" C4' OMC I2498 " 0.464 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.768 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.589 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.576 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.233 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.882 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.199 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.943 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.030 2.00e-02 2.50e+03 5.97e-01 8.01e+03 pdb=" C4' 2MG I2445 " -0.457 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.749 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.573 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.228 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.887 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.203 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.936 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.033 2.00e-02 2.50e+03 5.71e-01 7.33e+03 pdb=" C4' 2MG I1835 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.637 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.565 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.211 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.903 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.868 2.00e-02 2.50e+03 ... (remaining 8167 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 3269 2.11 - 2.73: 137498 2.73 - 3.35: 293842 3.35 - 3.98: 455844 3.98 - 4.60: 646533 Nonbonded interactions: 1536986 Sorted by model distance: nonbonded pdb=" OE1 GLU L 10 " pdb=" H GLU L 10 " model vdw 1.486 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.534 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.550 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.558 1.850 nonbonded pdb=" OP2 A I 320 " pdb=" HZ3 LYS M 132 " model vdw 1.569 1.850 ... (remaining 1536981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 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: 0.900 Extract box with map and model: 28.340 Check model and map are aligned: 1.200 Set scattering table: 0.760 Process input model: 417.350 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.250 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:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 465.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 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 0.391 81799 Z= 0.365 Angle : 0.564 51.339 125575 Z= 0.232 Chirality : 0.024 0.396 16420 Planarity : 0.022 0.601 4643 Dihedral : 23.669 176.801 50550 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.32 % Allowed : 23.57 % Favored : 76.11 % 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: 1.12 (0.26), residues: 1163 helix: 1.70 (0.35), residues: 246 sheet: 1.04 (0.38), residues: 205 loop : 0.41 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 248 HIS 0.002 0.001 HIS M 165 PHE 0.004 0.001 PHE N 127 TYR 0.006 0.001 TYR P 38 ARG 0.010 0.000 ARG R 41 *********************** 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 248 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 3.306 Fit side-chains revert: symmetry clash REVERT: M 136 GLN cc_start: 0.8372 (tp40) cc_final: 0.7717 (tm-30) REVERT: M 137 LYS cc_start: 0.8518 (tttp) cc_final: 0.8301 (tttt) outliers start: 3 outliers final: 2 residues processed: 245 average time/residue: 3.0118 time to fit residues: 933.4817 Evaluate side-chains 231 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 325 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 376 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN P 61 ASN Q 6 ASN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 81799 Z= 0.392 Angle : 0.628 27.377 125575 Z= 0.329 Chirality : 0.039 0.415 16420 Planarity : 0.007 0.142 4643 Dihedral : 23.533 179.723 48313 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.23 % Allowed : 21.13 % Favored : 76.65 % 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: 0.63 (0.25), residues: 1163 helix: 1.21 (0.32), residues: 267 sheet: 0.38 (0.35), residues: 219 loop : 0.22 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS L 35 PHE 0.012 0.001 PHE O 89 TYR 0.013 0.001 TYR P 38 ARG 0.005 0.001 ARG O 99 *********************** 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 262 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 136 GLN cc_start: 0.7979 (tp40) cc_final: 0.7309 (tm-30) REVERT: Q 37 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8592 (mtmp) outliers start: 21 outliers final: 12 residues processed: 247 average time/residue: 3.0010 time to fit residues: 942.4538 Evaluate side-chains 243 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 37 LYS 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: 9.9990 chunk 313 optimal weight: 0.0980 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 0.8980 chunk 336 optimal weight: 5.9990 chunk 374 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 302 optimal weight: 0.2980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN P 61 ASN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 81799 Z= 0.183 Angle : 0.562 27.090 125575 Z= 0.300 Chirality : 0.031 0.397 16420 Planarity : 0.006 0.129 4643 Dihedral : 23.521 176.173 48313 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.85 % Allowed : 22.29 % Favored : 76.86 % 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: 0.67 (0.25), residues: 1163 helix: 1.32 (0.32), residues: 267 sheet: 0.33 (0.35), residues: 215 loop : 0.24 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.003 0.001 HIS O 76 PHE 0.012 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.004 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 245 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 237 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 136 GLN cc_start: 0.8017 (tp40) cc_final: 0.7352 (tm-30) REVERT: N 42 ASN cc_start: 0.8942 (t0) cc_final: 0.8641 (t0) outliers start: 8 outliers final: 3 residues processed: 240 average time/residue: 3.0293 time to fit residues: 923.0954 Evaluate side-chains 247 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 244 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain O residue 81 ILE 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: 5.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 3.9990 chunk 401 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 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 134 ASN R 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 81799 Z= 0.406 Angle : 0.617 26.675 125575 Z= 0.328 Chirality : 0.038 0.419 16420 Planarity : 0.007 0.141 4643 Dihedral : 23.508 179.015 48312 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 2.02 % Allowed : 21.76 % Favored : 76.22 % 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: 0.45 (0.25), residues: 1163 helix: 1.22 (0.32), residues: 267 sheet: 0.19 (0.35), residues: 215 loop : 0.05 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS L 35 PHE 0.011 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.007 0.000 ARG O 99 *********************** 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 256 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 171 TYR cc_start: 0.8474 (m-80) cc_final: 0.8197 (m-80) REVERT: L 1 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.6686 (tmm) REVERT: M 136 GLN cc_start: 0.8103 (tp40) cc_final: 0.7429 (tm-30) REVERT: Q 46 ASP cc_start: 0.8680 (t70) cc_final: 0.8467 (t70) outliers start: 19 outliers final: 11 residues processed: 243 average time/residue: 3.0385 time to fit residues: 932.7825 Evaluate side-chains 243 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 231 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 3 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 342 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 360 optimal weight: 8.9990 chunk 101 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: N 42 ASN R 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 81799 Z= 0.400 Angle : 0.616 20.143 125575 Z= 0.331 Chirality : 0.039 0.406 16420 Planarity : 0.007 0.140 4643 Dihedral : 23.587 179.750 48312 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 2.02 % Allowed : 22.51 % Favored : 75.48 % 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: 0.24 (0.24), residues: 1163 helix: 1.15 (0.32), residues: 261 sheet: 0.08 (0.35), residues: 215 loop : -0.13 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.012 0.001 PHE M 183 TYR 0.017 0.001 TYR P 38 ARG 0.011 0.000 ARG M 170 *********************** 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 261 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.6900 (tmm) REVERT: M 136 GLN cc_start: 0.8201 (tp40) cc_final: 0.7537 (tm-30) REVERT: N 176 ASP cc_start: 0.8477 (m-30) cc_final: 0.8264 (m-30) REVERT: O 101 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9210 (mm) outliers start: 19 outliers final: 12 residues processed: 246 average time/residue: 3.2571 time to fit residues: 1032.6667 Evaluate side-chains 250 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain P residue 3 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 8.9990 chunk 333 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 210 optimal weight: 50.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN N 42 ASN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 81799 Z= 0.323 Angle : 0.597 16.848 125575 Z= 0.324 Chirality : 0.036 0.412 16420 Planarity : 0.007 0.138 4643 Dihedral : 23.604 179.981 48312 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 1.70 % Allowed : 23.57 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1163 helix: 1.13 (0.32), residues: 261 sheet: 0.04 (0.35), residues: 215 loop : -0.17 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.010 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 ARG 0.009 0.000 ARG O 99 *********************** 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 256 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 240 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 136 GLN cc_start: 0.8201 (tp40) cc_final: 0.7534 (tm-30) REVERT: N 176 ASP cc_start: 0.8473 (m-30) cc_final: 0.8262 (m-30) outliers start: 16 outliers final: 12 residues processed: 243 average time/residue: 3.0041 time to fit residues: 940.6490 Evaluate side-chains 247 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 235 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 3 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN N 42 ASN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 81799 Z= 0.332 Angle : 0.596 14.508 125575 Z= 0.323 Chirality : 0.036 0.412 16420 Planarity : 0.007 0.138 4643 Dihedral : 23.602 179.837 48312 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.59 % Allowed : 23.78 % Favored : 74.63 % 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: 0.19 (0.24), residues: 1163 helix: 1.14 (0.32), residues: 261 sheet: 0.04 (0.35), residues: 215 loop : -0.18 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.010 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 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 254 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 239 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 136 GLN cc_start: 0.8195 (tp40) cc_final: 0.7524 (tm-30) REVERT: N 176 ASP cc_start: 0.8477 (m-30) cc_final: 0.8264 (m-30) outliers start: 15 outliers final: 14 residues processed: 243 average time/residue: 3.0709 time to fit residues: 956.2226 Evaluate side-chains 248 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 234 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 3 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 314 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN 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: 0.8920 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 81799 Z= 0.296 Angle : 0.587 13.875 125575 Z= 0.320 Chirality : 0.035 0.411 16420 Planarity : 0.007 0.137 4643 Dihedral : 23.609 179.731 48312 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.38 % Allowed : 23.89 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1163 helix: 1.14 (0.32), residues: 261 sheet: 0.04 (0.35), residues: 215 loop : -0.18 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.010 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.006 0.000 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 247 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 136 GLN cc_start: 0.8195 (tp40) cc_final: 0.7522 (tm-30) REVERT: N 176 ASP cc_start: 0.8475 (m-30) cc_final: 0.8265 (m-30) outliers start: 13 outliers final: 12 residues processed: 237 average time/residue: 3.0416 time to fit residues: 921.7647 Evaluate side-chains 244 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 232 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 3 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 0.4980 chunk 383 optimal weight: 4.9990 chunk 349 optimal weight: 1.9990 chunk 372 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 292 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 352 optimal weight: 7.9990 chunk 371 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN R 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 81799 Z= 0.283 Angle : 0.586 13.779 125575 Z= 0.319 Chirality : 0.035 0.412 16420 Planarity : 0.007 0.137 4643 Dihedral : 23.610 179.661 48312 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.59 % Allowed : 23.89 % Favored : 74.52 % 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: 0.19 (0.24), residues: 1163 helix: 1.15 (0.32), residues: 261 sheet: 0.04 (0.35), residues: 215 loop : -0.18 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.011 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 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 246 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 231 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 136 GLN cc_start: 0.8197 (tp40) cc_final: 0.7523 (tm-30) REVERT: N 176 ASP cc_start: 0.8476 (m-30) cc_final: 0.8265 (m-30) outliers start: 15 outliers final: 14 residues processed: 235 average time/residue: 3.0790 time to fit residues: 922.1803 Evaluate side-chains 246 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 232 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 3 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 2.9990 chunk 394 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 413 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN N 42 ASN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 81799 Z= 0.295 Angle : 0.586 13.764 125575 Z= 0.319 Chirality : 0.035 0.411 16420 Planarity : 0.007 0.136 4643 Dihedral : 23.609 179.622 48312 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.59 % Allowed : 23.89 % Favored : 74.52 % 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: 0.20 (0.24), residues: 1163 helix: 1.16 (0.32), residues: 261 sheet: 0.04 (0.35), residues: 215 loop : -0.17 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.011 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.011 0.000 ARG O 99 ********************** 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 248 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 136 GLN cc_start: 0.8198 (tp40) cc_final: 0.7524 (tm-30) REVERT: N 176 ASP cc_start: 0.8476 (m-30) cc_final: 0.8266 (m-30) outliers start: 15 outliers final: 15 residues processed: 236 average time/residue: 3.0851 time to fit residues: 927.1424 Evaluate side-chains 246 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 231 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 3 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 338 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.070990 restraints weight = 257052.617| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 0.71 r_work: 0.2612 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 81799 Z= 0.393 Angle : 0.612 13.754 125575 Z= 0.329 Chirality : 0.038 0.415 16420 Planarity : 0.007 0.141 4643 Dihedral : 23.604 179.466 48312 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.59 % Allowed : 23.99 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1163 helix: 1.13 (0.32), residues: 261 sheet: 0.00 (0.35), residues: 215 loop : -0.27 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.011 0.001 PHE M 183 TYR 0.019 0.002 TYR P 38 ARG 0.008 0.001 ARG P 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35823.93 seconds wall clock time: 615 minutes 51.32 seconds (36951.32 seconds total)