Starting phenix.real_space_refine on Fri Jan 19 13:50:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e30_27852/01_2024/8e30_27852_neut_trim_updated.pdb" } resolution = 1.91 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= -0.022 sd= 0.849 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 3016 5.49 5 S 28 5.16 5 C 34599 2.51 5 N 13691 2.21 5 O 22581 1.98 5 F 2 1.80 5 H 41820 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 72": "OD1" <-> "OD2" Residue "K GLU 82": "OE1" <-> "OE2" Residue "K ASP 114": "OD1" <-> "OD2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K ASP 229": "OD1" <-> "OD2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M ARG 69": not complete - not flipped Residue "M ASP 116": "OD1" <-> "OD2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "M ASP 191": "OD1" <-> "OD2" Residue "M GLU 197": "OE1" <-> "OE2" Residue "M GLU 198": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 30": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 99": "OE1" <-> "OE2" Residue "N ASP 103": "OD1" <-> "OD2" Residue "N ASP 181": "OD1" <-> "OD2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O GLU 90": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "P ASP 22": "OD1" <-> "OD2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P ASP 94": "OD1" <-> "OD2" Residue "P ASP 109": "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-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 115737 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': 281, 'rna2p_pyr': 153, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1059} Link IDs: {'rna2p': 440, 'rna3p': 2457} Chain breaks: 1 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: 100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 50 Unusual residues: {'UE6': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 50 Unusual residues: {'UE6': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AUE6 I3001 " occ=0.50 ... (98 atoms not shown) pdb=" O7 BUE6 I3001 " occ=0.50 Time building chain proxies: 37.72, per 1000 atoms: 0.33 Number of scatterers: 115737 At special positions: 0 Unit cell: (229.656, 222.221, 190.829, 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 3016 15.00 F 2 9.00 O 22581 8.00 N 13691 7.00 C 34599 6.00 H 41820 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=0, symmetry=0 Time building additional restraints: 83.25 Conformation dependent library (CDL) restraints added in 2.7 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: 36 helices and 12 sheets defined 30.5% alpha, 15.2% beta 960 base pairs and 1572 stacking pairs defined. Time for finding SS restraints: 57.51 Creating SS restraints... Processing helix chain 'K' and resid 10 through 17 removed outlier: 7.942A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.706A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.633A 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 207 through 215 removed outlier: 3.830A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.311A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.080A 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 'L' and resid 37 through 42 removed outlier: 3.543A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.726A 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: 6.982A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.814A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.997A 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: 3.628A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 removed outlier: 6.505A pdb=" N THR M 53 " --> pdb=" O ARG M 49 " (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: 4.487A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU M 164 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N HIS M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 5.873A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.785A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.546A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.321A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.180A 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: 3.924A 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: 4.095A 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 122 removed outlier: 3.873A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 removed outlier: 4.470A pdb=" N LYS O 72 " --> pdb=" O ASN O 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 67 through 72' Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.525A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.668A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.877A 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: 4.166A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.442A 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 80 through 83 removed outlier: 3.615A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 162 through 165 removed outlier: 6.737A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.206A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'M' and resid 1 through 5 removed outlier: 3.556A pdb=" N LEU M 5 " --> pdb=" O SER M 10 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 42 through 47 removed outlier: 7.617A pdb=" N GLY M 42 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASP M 91 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 Processing sheet with id= 7, first strand: chain 'N' and resid 3 through 6 Processing sheet with id= 8, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.551A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 79 through 84 removed outlier: 5.839A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.713A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'O' and resid 14 through 19 Processing sheet with id= 12, first strand: chain 'P' and resid 2 through 8 261 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2425 hydrogen bonds 3808 hydrogen bond angles 0 basepair planarities 960 basepair parallelities 1572 stacking parallelities Total time for adding SS restraints: 137.39 Time building geometry restraints manager: 87.43 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: 41818 1.03 - 1.23: 630 1.23 - 1.42: 43281 1.42 - 1.62: 37851 1.62 - 1.81: 55 Bond restraints: 123635 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.413 0.389 2.00e-02 2.50e+03 3.79e+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 1.79e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C30AUE6 I3001 " pdb=" C32AUE6 I3001 " ideal model delta sigma weight residual 1.585 1.353 0.232 2.00e-02 2.50e+03 1.35e+02 ... (remaining 123630 not shown) Histogram of bond angle deviations from ideal: 68.01 - 81.40: 16 81.40 - 94.79: 4 94.79 - 108.17: 33512 108.17 - 121.56: 163087 121.56 - 134.94: 24773 Bond angle restraints: 221392 Sorted by residual: angle pdb=" C28BUE6 I3001 " pdb=" C15BUE6 I3001 " pdb=" N6 BUE6 I3001 " ideal model delta sigma weight residual 65.87 122.95 -57.08 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C28AUE6 I3001 " pdb=" C15AUE6 I3001 " pdb=" N6 AUE6 I3001 " ideal model delta sigma weight residual 65.87 121.61 -55.74 3.00e+00 1.11e-01 3.45e+02 angle pdb=" O3' A I1780 " pdb=" C3' A I1780 " pdb=" H3' A I1780 " ideal model delta sigma weight residual 109.00 68.01 40.99 3.00e+00 1.11e-01 1.87e+02 angle pdb=" O3' A I2062 " pdb=" C3' A I2062 " pdb=" H3' A I2062 " ideal model delta sigma weight residual 109.00 69.07 39.93 3.00e+00 1.11e-01 1.77e+02 angle pdb=" O3' A I1847 " pdb=" C3' A I1847 " pdb=" H3' A I1847 " ideal model delta sigma weight residual 109.00 74.30 34.70 3.00e+00 1.11e-01 1.34e+02 ... (remaining 221387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 52509 35.59 - 71.17: 5670 71.17 - 106.75: 807 106.75 - 142.34: 15 142.34 - 177.92: 6 Dihedral angle restraints: 59007 sinusoidal: 55357 harmonic: 3650 Sorted by residual: dihedral pdb=" CD ARG M 69 " pdb=" NE ARG M 69 " pdb=" CZ ARG M 69 " pdb=" NH1 ARG M 69 " ideal model delta sinusoidal sigma weight residual 0.00 177.92 -177.92 1 1.00e+01 1.00e-02 1.92e+02 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 54.91 177.09 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 40.39 -168.39 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 59004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.414: 16417 0.414 - 0.828: 4 0.828 - 1.242: 0 1.242 - 1.656: 0 1.656 - 2.070: 4 Chirality restraints: 16425 Sorted by residual: chirality pdb=" P C I2443 " pdb=" OP1 C I2443 " pdb=" OP2 C I2443 " pdb=" O5' C I2443 " both_signs ideal model delta sigma weight residual True 2.41 0.34 2.07 2.00e-01 2.50e+01 1.07e+02 chirality pdb=" P U I1778 " pdb=" OP1 U I1778 " pdb=" OP2 U I1778 " pdb=" O5' U I1778 " both_signs ideal model delta sigma weight residual True 2.41 0.34 2.07 2.00e-01 2.50e+01 1.07e+02 chirality pdb=" P C I 823 " pdb=" OP1 C I 823 " pdb=" OP2 C I 823 " pdb=" O5' C I 823 " both_signs ideal model delta sigma weight residual True 2.41 0.35 2.06 2.00e-01 2.50e+01 1.06e+02 ... (remaining 16422 not shown) Planarity restraints: 8170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.028 2.00e-02 2.50e+03 6.00e-01 8.11e+03 pdb=" C4' OMC I2498 " 0.465 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.772 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.586 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.574 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.234 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.878 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.198 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.946 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.044 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C4' 2MG I2445 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.627 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.587 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.201 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.921 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.229 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.047 2.00e-02 2.50e+03 5.73e-01 7.40e+03 pdb=" C4' OMG I2251 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.604 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.588 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.197 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.930 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.234 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.863 2.00e-02 2.50e+03 ... (remaining 8167 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 3536 2.13 - 2.74: 140909 2.74 - 3.36: 293396 3.36 - 3.98: 457439 3.98 - 4.60: 643211 Nonbonded interactions: 1538491 Sorted by model distance: nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.507 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.539 1.850 nonbonded pdb="HO2' G I 141 " pdb=" O4' A I 142 " model vdw 1.547 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.553 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.563 1.850 ... (remaining 1538486 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: 7.220 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: 0.840 Extract box with map and model: 28.590 Check model and map are aligned: 1.240 Set scattering table: 0.770 Process input model: 411.950 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.240 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 464.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.390 81815 Z= 0.360 Angle : 0.578 57.077 125604 Z= 0.248 Chirality : 0.042 2.070 16425 Planarity : 0.022 0.600 4642 Dihedral : 22.655 177.925 48183 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.50 % Rotamer: Outliers : 0.64 % Allowed : 17.73 % Favored : 81.63 % 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: 0.82 (0.26), residues: 1163 helix: 1.83 (0.33), residues: 264 sheet: 0.72 (0.36), residues: 211 loop : 0.03 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 248 HIS 0.002 0.001 HIS O 76 PHE 0.005 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.007 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 221 time to evaluate : 3.035 Fit side-chains revert: symmetry clash REVERT: M 145 ASP cc_start: 0.7911 (t0) cc_final: 0.7543 (t0) outliers start: 6 outliers final: 5 residues processed: 224 average time/residue: 2.8761 time to fit residues: 823.0433 Evaluate side-chains 219 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 214 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain P residue 108 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 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: 3.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN L 104 GLN M 195 GLN N 126 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 81815 Z= 0.367 Angle : 0.667 27.052 125604 Z= 0.345 Chirality : 0.051 2.144 16425 Planarity : 0.007 0.140 4642 Dihedral : 22.540 178.134 45948 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 1.59 % Allowed : 15.82 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1163 helix: 1.67 (0.32), residues: 267 sheet: 0.53 (0.34), residues: 215 loop : -0.13 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.009 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.004 0.001 ARG P 95 *********************** 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 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 3.055 Fit side-chains REVERT: M 145 ASP cc_start: 0.7854 (t0) cc_final: 0.7589 (t0) REVERT: N 88 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7889 (mt-10) outliers start: 15 outliers final: 10 residues processed: 218 average time/residue: 2.9432 time to fit residues: 818.1586 Evaluate side-chains 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 90 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 313 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 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 163 GLN L 104 GLN M 195 GLN N 185 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 81815 Z= 0.325 Angle : 0.649 27.129 125604 Z= 0.340 Chirality : 0.050 2.134 16425 Planarity : 0.007 0.141 4642 Dihedral : 22.557 178.766 45946 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.85 % Favored : 93.90 % Rotamer: Outliers : 1.80 % Allowed : 15.61 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1163 helix: 1.62 (0.33), residues: 267 sheet: 0.38 (0.34), residues: 215 loop : -0.24 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.014 0.001 TYR P 38 ARG 0.003 0.000 ARG K 63 *********************** 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 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 3.050 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 213 average time/residue: 3.1578 time to fit residues: 870.7143 Evaluate side-chains 224 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 378 optimal weight: 4.9990 chunk 401 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 359 optimal weight: 4.9990 chunk 108 optimal weight: 40.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN N 126 ASN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 81815 Z= 0.312 Angle : 0.646 27.153 125604 Z= 0.339 Chirality : 0.050 2.134 16425 Planarity : 0.007 0.138 4642 Dihedral : 22.549 179.065 45946 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.50 % Favored : 94.24 % Rotamer: Outliers : 2.02 % Allowed : 16.03 % Favored : 81.95 % 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: 0.41 (0.25), residues: 1163 helix: 1.58 (0.33), residues: 267 sheet: 0.39 (0.34), residues: 215 loop : -0.26 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.010 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.004 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 223 average time/residue: 3.0421 time to fit residues: 864.2680 Evaluate side-chains 219 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN P 31 GLN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 81815 Z= 0.327 Angle : 0.653 27.156 125604 Z= 0.343 Chirality : 0.050 2.137 16425 Planarity : 0.007 0.139 4642 Dihedral : 22.579 179.418 45946 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Rotamer: Outliers : 2.23 % Allowed : 14.65 % Favored : 83.12 % 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: 0.39 (0.25), residues: 1163 helix: 1.57 (0.33), residues: 267 sheet: 0.37 (0.34), residues: 215 loop : -0.26 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.015 0.001 TYR P 38 ARG 0.003 0.000 ARG R 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 3.155 Fit side-chains revert: symmetry clash REVERT: L 48 ARG cc_start: 0.9486 (OUTLIER) cc_final: 0.9237 (mtm180) REVERT: Q 34 SER cc_start: 0.9178 (t) cc_final: 0.8932 (p) outliers start: 21 outliers final: 18 residues processed: 217 average time/residue: 2.9703 time to fit residues: 820.3349 Evaluate side-chains 228 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER 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: 3.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 0.5980 chunk 333 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 210 optimal weight: 50.0000 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 163 GLN M 195 GLN N 126 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 81815 Z= 0.305 Angle : 0.648 27.147 125604 Z= 0.341 Chirality : 0.049 2.131 16425 Planarity : 0.007 0.139 4642 Dihedral : 22.584 179.644 45946 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 2.12 % Allowed : 15.71 % Favored : 82.17 % 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: 0.40 (0.25), residues: 1163 helix: 1.59 (0.33), residues: 267 sheet: 0.36 (0.34), residues: 215 loop : -0.26 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.010 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 ARG 0.004 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 ARG cc_start: 0.9484 (OUTLIER) cc_final: 0.9241 (mtm180) outliers start: 20 outliers final: 18 residues processed: 222 average time/residue: 3.0842 time to fit residues: 869.7271 Evaluate side-chains 217 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER 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: 5.9990 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: 3.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 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: K 163 GLN M 195 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 81815 Z= 0.346 Angle : 0.661 27.123 125604 Z= 0.347 Chirality : 0.051 2.143 16425 Planarity : 0.007 0.140 4642 Dihedral : 22.599 179.654 45946 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 2.23 % Allowed : 15.39 % Favored : 82.38 % 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: 0.30 (0.25), residues: 1163 helix: 1.40 (0.33), residues: 275 sheet: 0.38 (0.35), residues: 215 loop : -0.33 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.017 0.002 TYR P 38 ARG 0.007 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 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 3.194 Fit side-chains REVERT: L 48 ARG cc_start: 0.9492 (OUTLIER) cc_final: 0.9239 (mtm180) REVERT: N 39 ASP cc_start: 0.8551 (p0) cc_final: 0.8275 (p0) REVERT: O 96 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7771 (mmm-85) REVERT: Q 54 VAL cc_start: 0.8918 (t) cc_final: 0.8671 (m) outliers start: 21 outliers final: 15 residues processed: 211 average time/residue: 2.8312 time to fit residues: 763.4293 Evaluate side-chains 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 108 SER 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: 3.9990 chunk 120 optimal weight: 4.9990 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: 4.9990 chunk 314 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN N 126 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 81815 Z= 0.363 Angle : 0.666 27.115 125604 Z= 0.349 Chirality : 0.051 2.146 16425 Planarity : 0.007 0.141 4642 Dihedral : 22.623 179.836 45946 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 2.02 % Allowed : 15.50 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1163 helix: 1.34 (0.33), residues: 275 sheet: 0.30 (0.34), residues: 215 loop : -0.33 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.017 0.002 TYR P 38 ARG 0.004 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 229 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 3.023 Fit side-chains revert: symmetry clash REVERT: L 48 ARG cc_start: 0.9502 (OUTLIER) cc_final: 0.9251 (mtm180) REVERT: N 39 ASP cc_start: 0.8542 (p0) cc_final: 0.8267 (p0) REVERT: Q 54 VAL cc_start: 0.8932 (t) cc_final: 0.8690 (m) outliers start: 19 outliers final: 16 residues processed: 221 average time/residue: 3.0113 time to fit residues: 841.4871 Evaluate side-chains 217 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 2.9990 chunk 383 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 372 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN P 31 GLN R 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 81815 Z= 0.299 Angle : 0.654 27.168 125604 Z= 0.345 Chirality : 0.049 2.127 16425 Planarity : 0.007 0.139 4642 Dihedral : 22.635 179.881 45946 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.93 % Favored : 93.81 % Rotamer: Outliers : 1.70 % Allowed : 15.92 % Favored : 82.38 % 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: 0.26 (0.25), residues: 1163 helix: 1.36 (0.33), residues: 275 sheet: 0.30 (0.34), residues: 215 loop : -0.32 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE M 183 TYR 0.016 0.001 TYR P 38 ARG 0.006 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 216 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 3.042 Fit side-chains revert: symmetry clash REVERT: L 48 ARG cc_start: 0.9496 (OUTLIER) cc_final: 0.9242 (mtm180) REVERT: N 39 ASP cc_start: 0.8539 (p0) cc_final: 0.8262 (p0) REVERT: Q 54 VAL cc_start: 0.8929 (t) cc_final: 0.8688 (m) outliers start: 16 outliers final: 15 residues processed: 209 average time/residue: 3.0027 time to fit residues: 800.1003 Evaluate side-chains 224 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER 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: 5.9990 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 413 optimal weight: 0.8980 chunk 380 optimal weight: 2.9990 chunk 329 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 81815 Z= 0.224 Angle : 0.640 27.177 125604 Z= 0.340 Chirality : 0.048 2.113 16425 Planarity : 0.007 0.137 4642 Dihedral : 22.654 179.885 45946 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 1.80 % Allowed : 16.03 % Favored : 82.17 % 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: 0.27 (0.25), residues: 1163 helix: 1.36 (0.33), residues: 276 sheet: 0.30 (0.35), residues: 215 loop : -0.32 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 ARG 0.008 0.000 ARG P 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 ARG cc_start: 0.9490 (OUTLIER) cc_final: 0.9234 (mtm180) REVERT: N 39 ASP cc_start: 0.8527 (p0) cc_final: 0.8252 (p0) REVERT: Q 54 VAL cc_start: 0.8924 (t) cc_final: 0.8682 (m) outliers start: 17 outliers final: 16 residues processed: 219 average time/residue: 2.9733 time to fit residues: 826.1088 Evaluate side-chains 217 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER 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: 1.9990 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: 0.2980 chunk 138 optimal weight: 5.9990 chunk 338 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.062575 restraints weight = 258599.641| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 0.47 r_work: 0.2582 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 81815 Z= 0.256 Angle : 0.641 27.134 125604 Z= 0.339 Chirality : 0.049 2.123 16425 Planarity : 0.007 0.136 4642 Dihedral : 22.647 179.878 45946 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 1.91 % Allowed : 15.92 % Favored : 82.17 % 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: 0.27 (0.25), residues: 1163 helix: 1.37 (0.33), residues: 276 sheet: 0.30 (0.35), residues: 215 loop : -0.32 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 ARG 0.004 0.000 ARG P 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38049.76 seconds wall clock time: 653 minutes 13.02 seconds (39193.02 seconds total)