Starting phenix.real_space_refine on Tue Mar 12 18:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/03_2024/8e42_27877_neut_trim_updated.pdb" } resolution = 2.29 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= -0.028 sd= 0.674 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 3016 5.49 5 S 29 5.16 5 C 34597 2.51 5 N 13678 2.21 5 O 22583 1.98 5 H 41815 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 98": "OD1" <-> "OD2" Residue "K ASP 114": "OD1" <-> "OD2" Residue "K ASP 121": "OD1" <-> "OD2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K GLU 236": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "M ASP 22": "OD1" <-> "OD2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "N ASP 18": "OD1" <-> "OD2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 99": "OE1" <-> "OE2" Residue "N ASP 181": "OD1" <-> "OD2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O ASP 49": "OD1" <-> "OD2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 90": "OE1" <-> "OE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "O ASP 141": "OD1" <-> "OD2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ASP 77": "OD1" <-> "OD2" Residue "Q GLU 36": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 115718 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1385, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 438, 'rna3p': 2459} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3805 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 46} Link IDs: {'rna2p': 16, 'rna3p': 101} 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'MUL': 1, 'ZIT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 38.72, per 1000 atoms: 0.33 Number of scatterers: 115718 At special positions: 0 Unit cell: (229.91, 222.44, 190.9, 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 29 16.00 P 3016 15.00 O 22583 8.00 N 13678 7.00 C 34597 6.00 H 41815 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: 80.25 Conformation dependent library (CDL) restraints added in 2.6 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 16 sheets defined 30.0% alpha, 17.8% beta 923 base pairs and 1592 stacking pairs defined. Time for finding SS restraints: 53.27 Creating SS restraints... Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.560A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.019A 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: 5.525A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 136 removed outlier: 3.515A 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: 3.824A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.240A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 4.989A 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 268 removed outlier: 7.501A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 268' Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.531A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.712A 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: 6.849A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.522A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' 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: 3.621A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 5.934A 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 163 removed outlier: 4.538A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.527A 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: 5.465A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.887A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.688A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.278A 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: 3.676A 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: 4.188A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.619A 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 123 removed outlier: 3.872A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS O 123 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.504A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.664A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.826A 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: 4.126A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.425A 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: 3.594A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE K 74 " --> pdb=" O SER K 118 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER K 118 " --> pdb=" O ILE K 74 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.141A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.063A 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: 3.857A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 1 through 6 removed outlier: 3.610A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 44 through 47 removed outlier: 6.878A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.641A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 3 through 6 Processing sheet with id= 9, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.604A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.115A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.660A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.809A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'O' and resid 74 through 78 removed outlier: 7.030A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'P' and resid 2 through 8 removed outlier: 6.926A pdb=" N VAL P 106 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'P' and resid 80 through 88 removed outlier: 3.711A pdb=" N THR P 100 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG P 92 " --> pdb=" O ARG P 88 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.501A pdb=" N SER Q 29 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS Q 37 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASP Q 31 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2303 hydrogen bonds 3622 hydrogen bond angles 0 basepair planarities 923 basepair parallelities 1592 stacking parallelities Total time for adding SS restraints: 140.78 Time building geometry restraints manager: 84.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 41813 1.04 - 1.24: 2485 1.24 - 1.43: 43606 1.43 - 1.63: 35654 1.63 - 1.83: 56 Bond restraints: 123614 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 3.81e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+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 1.76e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.349 -0.194 2.00e-02 2.50e+03 9.43e+01 ... (remaining 123609 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.58: 17955 106.58 - 113.65: 121483 113.65 - 120.71: 50281 120.71 - 127.78: 26566 127.78 - 134.84: 5092 Bond angle restraints: 221377 Sorted by residual: angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 126.02 -19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C4 OMG I2251 " ideal model delta sigma weight residual 108.29 126.51 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C8 OMG I2251 " ideal model delta sigma weight residual 142.82 126.07 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" C1' G7M I2069 " pdb=" N9 G7M I2069 " pdb=" C8 G7M I2069 " ideal model delta sigma weight residual 112.61 129.24 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" C1' 2MG I2445 " pdb=" N9 2MG I2445 " pdb=" C8 2MG I2445 " ideal model delta sigma weight residual 110.07 125.87 -15.80 3.00e+00 1.11e-01 2.78e+01 ... (remaining 221372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 53310 36.00 - 72.00: 7313 72.00 - 108.00: 866 108.00 - 144.00: 63 144.00 - 180.00: 726 Dihedral angle restraints: 62278 sinusoidal: 58628 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 232.00 54.13 177.87 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 43.58 -171.58 1 1.70e+01 3.46e-03 6.61e+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 94.35 105.65 1 1.50e+01 4.44e-03 5.42e+01 ... (remaining 62275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.093: 16438 1.093 - 2.187: 0 2.187 - 3.280: 0 3.280 - 4.373: 0 4.373 - 5.466: 3 Chirality restraints: 16441 Sorted by residual: chirality pdb=" C3B ZIT I3002 " pdb=" C2B ZIT I3002 " pdb=" C4B ZIT I3002 " pdb=" C7B ZIT I3002 " both_signs ideal model delta sigma weight residual False 2.67 -2.79 5.47 2.00e-01 2.50e+01 7.47e+02 chirality pdb=" C6 ZIT I3002 " pdb=" C19 ZIT I3002 " pdb=" C5 ZIT I3002 " pdb=" C7 ZIT I3002 " both_signs ideal model delta sigma weight residual False -2.74 2.72 -5.46 2.00e-01 2.50e+01 7.45e+02 chirality pdb=" C1B ZIT I3002 " pdb=" C2B ZIT I3002 " pdb=" O1B ZIT I3002 " pdb=" O5B ZIT I3002 " both_signs ideal model delta sigma weight residual False -2.37 2.23 -4.60 2.00e-01 2.50e+01 5.30e+02 ... (remaining 16438 not shown) Planarity restraints: 8153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.028 2.00e-02 2.50e+03 6.01e-01 8.13e+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 " -0.586 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.577 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.232 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.883 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.199 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.024 2.00e-02 2.50e+03 5.90e-01 7.82e+03 pdb=" C4' 2MG I2445 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.730 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.565 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.227 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.884 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.209 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.039 2.00e-02 2.50e+03 5.72e-01 7.35e+03 pdb=" C4' OMG I2251 " 0.433 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.620 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.575 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.205 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.916 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.232 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.865 2.00e-02 2.50e+03 ... (remaining 8150 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 3318 2.14 - 2.75: 143234 2.75 - 3.37: 291597 3.37 - 3.98: 455681 3.98 - 4.60: 636504 Nonbonded interactions: 1530334 Sorted by model distance: nonbonded pdb=" OE1 GLU M 16 " pdb=" H GLU M 16 " model vdw 1.519 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.529 1.850 nonbonded pdb=" OP2 G I2581 " pdb=" H22 G I2581 " model vdw 1.534 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.571 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.576 1.850 ... (remaining 1530329 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=1.00 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.940 Extract box with map and model: 28.340 Check model and map are aligned: 1.440 Set scattering table: 0.780 Process input model: 405.950 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.270 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: 0.030 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 455.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.390 81799 Z= 0.310 Angle : 0.373 19.702 125598 Z= 0.187 Chirality : 0.074 5.466 16441 Planarity : 0.022 0.601 4627 Dihedral : 23.539 177.871 50616 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.53 % Allowed : 17.62 % Favored : 81.85 % 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: 0.92 (0.26), residues: 1163 helix: 1.96 (0.35), residues: 259 sheet: 0.59 (0.34), residues: 228 loop : 0.16 (0.25), residues: 676 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 0.003 0.001 PHE K 240 TYR 0.007 0.001 TYR L 58 ARG 0.010 0.000 ARG M 21 *********************** 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 240 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 235 time to evaluate : 3.076 Fit side-chains revert: symmetry clash REVERT: N 86 GLU cc_start: 0.8076 (tp30) cc_final: 0.7795 (tm-30) REVERT: R 25 LYS cc_start: 0.9036 (tmmt) cc_final: 0.8817 (tmtt) outliers start: 5 outliers final: 4 residues processed: 237 average time/residue: 2.8622 time to fit residues: 870.4057 Evaluate side-chains 234 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 230 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 0.3980 chunk 314 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 4.9990 chunk 325 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 GLN N 130 GLN O 138 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 81799 Z= 0.331 Angle : 0.619 27.099 125598 Z= 0.327 Chirality : 0.043 2.070 16441 Planarity : 0.007 0.136 4627 Dihedral : 23.428 178.862 48385 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.64 % Allowed : 18.15 % Favored : 81.21 % 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: 1.58 (0.33), residues: 266 sheet: 0.34 (0.35), residues: 205 loop : 0.10 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.009 0.001 PHE M 183 TYR 0.010 0.001 TYR P 38 ARG 0.003 0.000 ARG O 27 *********************** 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 232 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 229 average time/residue: 3.0065 time to fit residues: 886.5127 Evaluate side-chains 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 313 optimal weight: 0.0870 chunk 256 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 2.9990 chunk 336 optimal weight: 0.8980 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 81799 Z= 0.211 Angle : 0.566 25.444 125598 Z= 0.305 Chirality : 0.039 1.926 16441 Planarity : 0.006 0.128 4627 Dihedral : 23.452 178.499 48381 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.53 % Allowed : 17.20 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1163 helix: 1.59 (0.33), residues: 267 sheet: 0.18 (0.35), residues: 204 loop : 0.08 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.004 0.001 HIS O 76 PHE 0.008 0.001 PHE M 183 TYR 0.006 0.001 TYR K 103 ARG 0.004 0.000 ARG R 35 *********************** 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 236 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 231 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 233 average time/residue: 2.9789 time to fit residues: 885.4092 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 218 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain P residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 4.9990 chunk 108 optimal weight: 40.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 81799 Z= 0.374 Angle : 0.623 26.244 125598 Z= 0.332 Chirality : 0.043 1.887 16441 Planarity : 0.007 0.137 4627 Dihedral : 23.463 179.356 48376 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.64 % Allowed : 17.83 % Favored : 81.53 % 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: 0.37 (0.25), residues: 1163 helix: 1.37 (0.33), residues: 273 sheet: 0.01 (0.34), residues: 219 loop : -0.07 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.005 0.001 HIS P 60 PHE 0.009 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.004 0.000 ARG O 27 *********************** 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 224 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 218 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 99 GLU cc_start: 0.7855 (pm20) cc_final: 0.7495 (pm20) REVERT: P 28 LYS cc_start: 0.8733 (mtmp) cc_final: 0.8510 (mtmm) outliers start: 6 outliers final: 4 residues processed: 220 average time/residue: 2.9711 time to fit residues: 841.2401 Evaluate side-chains 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain P residue 69 LEU 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: 3.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 81799 Z= 0.336 Angle : 0.612 25.942 125598 Z= 0.326 Chirality : 0.042 1.903 16441 Planarity : 0.007 0.134 4627 Dihedral : 23.525 179.434 48376 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.96 % Allowed : 17.20 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1163 helix: 1.34 (0.33), residues: 270 sheet: -0.02 (0.34), residues: 213 loop : -0.19 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.006 0.001 HIS P 60 PHE 0.012 0.001 PHE K 240 TYR 0.010 0.001 TYR Q 49 ARG 0.003 0.000 ARG L 78 *********************** 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 238 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 229 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 99 GLU cc_start: 0.7763 (pm20) cc_final: 0.7381 (pm20) REVERT: P 28 LYS cc_start: 0.8639 (mtmp) cc_final: 0.8401 (mtmm) outliers start: 9 outliers final: 5 residues processed: 232 average time/residue: 2.9661 time to fit residues: 878.2198 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain P residue 69 LEU 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: 4.9990 chunk 79 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 333 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 210 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.1752 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= 0.423 Angle : 0.650 26.351 125598 Z= 0.347 Chirality : 0.045 1.900 16441 Planarity : 0.007 0.142 4627 Dihedral : 23.561 178.424 48376 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.06 % Allowed : 18.37 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1163 helix: 1.30 (0.33), residues: 268 sheet: -0.11 (0.34), residues: 211 loop : -0.26 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.007 0.001 HIS P 60 PHE 0.011 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.004 0.000 ARG O 27 *********************** 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 224 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 81 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8486 (mt-10) REVERT: N 99 GLU cc_start: 0.7753 (pm20) cc_final: 0.7384 (pm20) REVERT: P 28 LYS cc_start: 0.8714 (mtmp) cc_final: 0.8484 (mtmm) outliers start: 10 outliers final: 7 residues processed: 219 average time/residue: 2.9474 time to fit residues: 821.2403 Evaluate side-chains 219 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 212 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 81 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 338 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 81799 Z= 0.328 Angle : 0.629 26.283 125598 Z= 0.337 Chirality : 0.043 1.907 16441 Planarity : 0.007 0.138 4627 Dihedral : 23.583 178.525 48376 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.96 % Allowed : 18.58 % Favored : 80.47 % 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: 0.14 (0.25), residues: 1163 helix: 1.34 (0.33), residues: 268 sheet: -0.13 (0.34), residues: 213 loop : -0.28 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS P 60 PHE 0.011 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.002 0.000 ARG O 27 *********************** 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 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 81 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8466 (mt-10) REVERT: P 28 LYS cc_start: 0.8610 (mtmp) cc_final: 0.8401 (mtmm) outliers start: 9 outliers final: 6 residues processed: 222 average time/residue: 3.0269 time to fit residues: 854.1349 Evaluate side-chains 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain P residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1877 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= 0.423 Angle : 0.647 26.374 125598 Z= 0.344 Chirality : 0.045 1.918 16441 Planarity : 0.007 0.140 4627 Dihedral : 23.589 178.903 48376 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.96 % Allowed : 18.37 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1163 helix: 1.31 (0.33), residues: 266 sheet: -0.12 (0.34), residues: 201 loop : -0.31 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.008 0.001 HIS P 60 PHE 0.012 0.001 PHE K 240 TYR 0.012 0.002 TYR Q 49 ARG 0.004 0.000 ARG O 27 *********************** 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 235 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 226 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 81 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8480 (mt-10) outliers start: 9 outliers final: 7 residues processed: 230 average time/residue: 3.1617 time to fit residues: 941.5980 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 156 ASN Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain P residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 0.5980 chunk 383 optimal weight: 4.9990 chunk 349 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 352 optimal weight: 1.9990 chunk 371 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 81799 Z= 0.232 Angle : 0.609 26.320 125598 Z= 0.328 Chirality : 0.040 1.920 16441 Planarity : 0.006 0.132 4627 Dihedral : 23.648 179.144 48376 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.06 % Allowed : 18.68 % Favored : 80.25 % 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: 0.11 (0.25), residues: 1163 helix: 1.31 (0.33), residues: 270 sheet: -0.23 (0.34), residues: 216 loop : -0.27 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS P 60 PHE 0.010 0.001 PHE M 183 TYR 0.010 0.001 TYR P 38 ARG 0.002 0.000 ARG O 27 *********************** 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 227 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 217 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 81 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8456 (mt-10) outliers start: 10 outliers final: 6 residues processed: 220 average time/residue: 3.0073 time to fit residues: 853.7175 Evaluate side-chains 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain P residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 3.9990 chunk 394 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 413 optimal weight: 4.9990 chunk 380 optimal weight: 0.8980 chunk 329 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 81799 Z= 0.261 Angle : 0.597 26.271 125598 Z= 0.321 Chirality : 0.040 1.918 16441 Planarity : 0.006 0.131 4627 Dihedral : 23.559 179.826 48376 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.42 % Allowed : 19.64 % Favored : 79.94 % 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: 0.19 (0.25), residues: 1163 helix: 1.33 (0.33), residues: 270 sheet: -0.11 (0.34), residues: 213 loop : -0.23 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.004 0.001 HIS L 35 PHE 0.009 0.001 PHE M 183 TYR 0.010 0.001 TYR Q 49 ARG 0.002 0.000 ARG O 27 ********************** 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 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 81 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8435 (mt-10) REVERT: P 31 GLN cc_start: 0.8360 (mt0) cc_final: 0.7965 (pt0) outliers start: 4 outliers final: 3 residues processed: 221 average time/residue: 3.0801 time to fit residues: 877.4834 Evaluate side-chains 218 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 56 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 4.9990 chunk 350 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.061507 restraints weight = 230381.387| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 0.50 r_work: 0.2522 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 81799 Z= 0.337 Angle : 0.614 26.419 125598 Z= 0.329 Chirality : 0.042 1.919 16441 Planarity : 0.007 0.136 4627 Dihedral : 23.554 179.329 48376 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.53 % Allowed : 19.43 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1163 helix: 1.34 (0.33), residues: 268 sheet: -0.15 (0.34), residues: 211 loop : -0.24 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS P 60 PHE 0.011 0.001 PHE M 183 TYR 0.011 0.001 TYR P 38 ARG 0.003 0.000 ARG O 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33627.27 seconds wall clock time: 578 minutes 31.03 seconds (34711.03 seconds total)