Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 23 09:31:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/08_2023/8cgu_16651_updated.pdb" } resolution = 1.89 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= 0.000 sd= 0.002 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 K 24 8.98 5 P 1078 5.49 5 Mg 58 5.21 5 S 40 5.16 5 C 16620 2.51 5 N 6215 2.21 5 O 11161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 14": "NH1" <-> "NH2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F ARG 2": "NH1" <-> "NH2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "U ARG 55": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 35196 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 22517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 22517 Classifications: {'RNA': 1047} Modifications used: {'rna2p': 1, 'rna2p_pur': 79, 'rna2p_pyr': 51, 'rna3p': 7, 'rna3p_pur': 529, 'rna3p_pyr': 380} Link IDs: {'rna2p': 131, 'rna3p': 915} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 831 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 827 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 386 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Chain: "a" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 4, 'rna3p': 2, 'rna3p_pur': 13, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 26} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 204 Unusual residues: {' K': 22, ' MG': 58, 'LLL': 4} Classifications: {'undetermined': 84} Link IDs: {None: 83} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1631, 1631 Classifications: {'water': 1631} Link IDs: {None: 1630} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "O" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "U" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 17.79, per 1000 atoms: 0.51 Number of scatterers: 35196 At special positions: 0 Unit cell: (158.213, 201.362, 123.391, 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) K 24 19.00 S 40 16.00 P 1078 15.00 Mg 58 11.99 O 11161 8.00 N 6215 7.00 C 16620 6.00 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: 21.19 Conformation dependent library (CDL) restraints added in 1.9 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 12 sheets defined 37.8% alpha, 19.6% beta 374 base pairs and 615 stacking pairs defined. Time for finding SS restraints: 22.00 Creating SS restraints... Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.849A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'E' and resid 56 through 69 removed outlier: 3.524A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.550A pdb=" N ARG E 112 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 114 " --> pdb=" O MET E 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 117 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 18 through 31 Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 95 through 98 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 60 through 73 Processing helix chain 'K' and resid 91 through 103 removed outlier: 4.416A pdb=" N GLU K 94 " --> pdb=" O PRO K 91 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER K 95 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR K 96 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG K 98 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 116 No H-bonds generated for 'chain 'L' and resid 114 through 116' Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.437A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 3.790A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 54 through 62 Processing helix chain 'P' and resid 69 through 78 Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.898A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.570A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 removed outlier: 3.717A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 26 Processing helix chain 'U' and resid 28 through 34 Processing helix chain 'U' and resid 41 through 55 Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= B, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.716A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.568A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS F 11 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL F 84 " --> pdb=" O HIS F 11 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 35 through 41 removed outlier: 6.479A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.625A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 75 through 77 removed outlier: 6.660A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 106 through 112 removed outlier: 6.983A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 29 through 33 removed outlier: 9.380A pdb=" N ARG L 94 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR L 64 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS L 96 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR L 66 " --> pdb=" O HIS L 96 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 2 through 11 removed outlier: 3.559A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 8 through 11 removed outlier: 9.364A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLU Q 26 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLY Q 10 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.118A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 934 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 374 basepair parallelities 615 stacking parallelities Total time for adding SS restraints: 69.97 Time building geometry restraints manager: 21.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4957 1.34 - 1.46: 16857 1.46 - 1.58: 12137 1.58 - 1.70: 2149 1.70 - 1.83: 68 Bond restraints: 36168 Sorted by residual: bond pdb=" O4' 3TD a1915 " pdb=" C1' 3TD a1915 " ideal model delta sigma weight residual 1.652 1.437 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C2' 3TD a1915 " pdb=" C1' 3TD a1915 " ideal model delta sigma weight residual 1.329 1.535 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C5 4OC A1402 " pdb=" C6 4OC A1402 " ideal model delta sigma weight residual 1.512 1.342 0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" C5 UR3 A1498 " pdb=" C6 UR3 A1498 " ideal model delta sigma weight residual 1.505 1.342 0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" C2 4OC A1402 " pdb=" N3 4OC A1402 " ideal model delta sigma weight residual 1.507 1.357 0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 36163 not shown) Histogram of bond angle deviations from ideal: 87.08 - 96.57: 44 96.57 - 106.06: 6832 106.06 - 115.55: 23588 115.55 - 125.04: 19197 125.04 - 134.53: 4544 Bond angle restraints: 54205 Sorted by residual: angle pdb=" O3' G A1529 " pdb=" P G A1530 " pdb=" O5' G A1530 " ideal model delta sigma weight residual 104.00 87.08 16.92 1.50e+00 4.44e-01 1.27e+02 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 125.94 -30.98 3.00e+00 1.11e-01 1.07e+02 angle pdb=" O3' C a1905 " pdb=" P G a1906 " pdb=" O5' G a1906 " ideal model delta sigma weight residual 104.00 89.32 14.68 1.50e+00 4.44e-01 9.57e+01 angle pdb=" O3' A A 746 " pdb=" P A A 747 " pdb=" O5' A A 747 " ideal model delta sigma weight residual 104.00 90.72 13.28 1.50e+00 4.44e-01 7.84e+01 angle pdb=" O3' C A 176 " pdb=" P G A 177 " pdb=" O5' G A 177 " ideal model delta sigma weight residual 104.00 91.08 12.92 1.50e+00 4.44e-01 7.41e+01 ... (remaining 54200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 18644 35.74 - 71.49: 440 71.49 - 107.23: 37 107.23 - 142.97: 1 142.97 - 178.71: 4 Dihedral angle restraints: 19126 sinusoidal: 15495 harmonic: 3631 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 56.16 143.84 1 1.50e+01 4.44e-03 7.71e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 62.68 137.32 1 1.50e+01 4.44e-03 7.40e+01 dihedral pdb=" O4' U A 421 " pdb=" C1' U A 421 " pdb=" N1 U A 421 " pdb=" C2 U A 421 " ideal model delta sinusoidal sigma weight residual 232.00 53.34 178.66 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 19123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5032 0.126 - 0.253: 1848 0.253 - 0.379: 42 0.379 - 0.506: 3 0.506 - 0.632: 6 Chirality restraints: 6931 Sorted by residual: chirality pdb=" P U A1390 " pdb=" OP1 U A1390 " pdb=" OP2 U A1390 " pdb=" O5' U A1390 " both_signs ideal model delta sigma weight residual True 2.41 -3.04 -0.63 2.00e-01 2.50e+01 9.99e+00 chirality pdb=" P C a1905 " pdb=" OP1 C a1905 " pdb=" OP2 C a1905 " pdb=" O5' C a1905 " both_signs ideal model delta sigma weight residual True 2.41 -3.03 -0.62 2.00e-01 2.50e+01 9.59e+00 chirality pdb=" P U A 92 " pdb=" OP1 U A 92 " pdb=" OP2 U A 92 " pdb=" O5' U A 92 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 6928 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " 0.091 2.00e-02 2.50e+03 6.15e-01 8.52e+03 pdb=" C4' 5MC A1407 " 0.443 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " 0.634 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " -0.641 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " -0.688 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " -0.138 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " 0.997 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " 0.227 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " -0.923 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.101 2.00e-02 2.50e+03 6.03e-01 8.19e+03 pdb=" C4' 2MG A1516 " 0.429 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.592 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.642 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.672 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.122 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.991 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.227 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.904 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 587 " -0.130 2.00e-02 2.50e+03 5.19e-02 8.07e+01 pdb=" N9 G A 587 " 0.097 2.00e-02 2.50e+03 pdb=" C8 G A 587 " 0.015 2.00e-02 2.50e+03 pdb=" N7 G A 587 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G A 587 " 0.015 2.00e-02 2.50e+03 pdb=" C6 G A 587 " -0.034 2.00e-02 2.50e+03 pdb=" O6 G A 587 " -0.031 2.00e-02 2.50e+03 pdb=" N1 G A 587 " -0.024 2.00e-02 2.50e+03 pdb=" C2 G A 587 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 587 " 0.011 2.00e-02 2.50e+03 pdb=" N3 G A 587 " 0.034 2.00e-02 2.50e+03 pdb=" C4 G A 587 " 0.036 2.00e-02 2.50e+03 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.54: 434 2.54 - 3.19: 31996 3.19 - 3.84: 91886 3.84 - 4.49: 127134 4.49 - 5.14: 164482 Nonbonded interactions: 415932 Sorted by model distance: nonbonded pdb=" OP2 A A 509 " pdb="MG MG A1624 " model vdw 1.895 2.170 nonbonded pdb=" OP1 G A 21 " pdb="MG MG A1634 " model vdw 1.910 2.170 nonbonded pdb="MG MG A1645 " pdb=" O HOH A2051 " model vdw 1.915 2.170 nonbonded pdb="MG MG A1610 " pdb=" O HOH A2083 " model vdw 1.919 2.170 nonbonded pdb=" OP1 C A 578 " pdb="MG MG A1607 " model vdw 1.925 2.170 ... (remaining 415927 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 24.840 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 161.710 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.009 0.215 36168 Z= 0.535 Angle : 1.589 30.983 54205 Z= 0.963 Chirality : 0.107 0.632 6931 Planarity : 0.024 0.615 2832 Dihedral : 13.274 178.715 16780 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.33 % 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: -0.61 (0.21), residues: 1233 helix: -0.14 (0.20), residues: 502 sheet: -0.27 (0.32), residues: 227 loop : -0.55 (0.24), residues: 504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 315 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 318 average time/residue: 2.0989 time to fit residues: 768.4824 Evaluate side-chains 256 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.1172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 116 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 40 GLN E 121 HIS E 146 ASN F 11 HIS H 18 GLN K 81 ASN L 20 ASN O 35 GLN Q 9 GLN R 19 GLN R 31 ASN T 3 ASN T 48 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 36168 Z= 0.132 Angle : 0.580 12.969 54205 Z= 0.320 Chirality : 0.035 0.326 6931 Planarity : 0.005 0.125 2832 Dihedral : 12.184 176.417 14289 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1233 helix: 1.92 (0.23), residues: 493 sheet: 0.16 (0.33), residues: 237 loop : 0.05 (0.27), residues: 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 260 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 262 average time/residue: 2.1437 time to fit residues: 648.4174 Evaluate side-chains 245 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 2.261 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.3317 time to fit residues: 2.9643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 223 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN E 12 GLN E 73 ASN E 78 ASN E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 48 GLN T 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 36168 Z= 0.290 Angle : 0.789 15.859 54205 Z= 0.406 Chirality : 0.042 0.325 6931 Planarity : 0.007 0.136 2832 Dihedral : 12.301 173.967 14289 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1233 helix: 1.62 (0.22), residues: 499 sheet: 0.19 (0.33), residues: 232 loop : 0.08 (0.27), residues: 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 247 time to evaluate : 2.222 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 248 average time/residue: 2.0979 time to fit residues: 600.6636 Evaluate side-chains 244 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.1043 time to fit residues: 5.0157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 7.9990 chunk 155 optimal weight: 0.0980 chunk 107 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 207 optimal weight: 0.4980 chunk 219 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 36168 Z= 0.145 Angle : 0.599 12.920 54205 Z= 0.329 Chirality : 0.036 0.362 6931 Planarity : 0.006 0.129 2832 Dihedral : 12.254 173.899 14289 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1233 helix: 1.85 (0.22), residues: 495 sheet: 0.27 (0.33), residues: 229 loop : 0.10 (0.27), residues: 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 244 time to evaluate : 2.116 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 248 average time/residue: 2.1146 time to fit residues: 605.5504 Evaluate side-chains 238 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.3317 time to fit residues: 2.8320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 36168 Z= 0.341 Angle : 0.850 16.350 54205 Z= 0.431 Chirality : 0.045 0.310 6931 Planarity : 0.008 0.137 2832 Dihedral : 12.331 173.398 14289 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.93 (0.23), residues: 1233 helix: 1.48 (0.22), residues: 494 sheet: 0.24 (0.33), residues: 235 loop : 0.06 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 2.084 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 246 average time/residue: 2.0433 time to fit residues: 581.4653 Evaluate side-chains 237 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 1.851 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 1.1620 time to fit residues: 6.5908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 36168 Z= 0.311 Angle : 0.807 15.852 54205 Z= 0.413 Chirality : 0.043 0.318 6931 Planarity : 0.007 0.136 2832 Dihedral : 12.317 173.273 14289 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.84 (0.23), residues: 1233 helix: 1.40 (0.22), residues: 495 sheet: 0.22 (0.33), residues: 235 loop : 0.00 (0.27), residues: 503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 239 time to evaluate : 2.027 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 240 average time/residue: 2.0848 time to fit residues: 577.5571 Evaluate side-chains 237 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.5228 time to fit residues: 5.8236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 122 optimal weight: 0.0370 chunk 218 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 36168 Z= 0.197 Angle : 0.658 14.299 54205 Z= 0.352 Chirality : 0.037 0.322 6931 Planarity : 0.006 0.130 2832 Dihedral : 12.202 173.681 14289 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1233 helix: 1.73 (0.23), residues: 495 sheet: 0.32 (0.33), residues: 234 loop : 0.09 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 246 time to evaluate : 2.168 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 248 average time/residue: 2.1371 time to fit residues: 611.0239 Evaluate side-chains 238 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 2.026 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.9058 time to fit residues: 4.4268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 0.0170 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 36168 Z= 0.279 Angle : 0.766 15.829 54205 Z= 0.397 Chirality : 0.041 0.317 6931 Planarity : 0.007 0.134 2832 Dihedral : 12.274 173.257 14289 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.96 (0.23), residues: 1233 helix: 1.52 (0.22), residues: 495 sheet: 0.30 (0.34), residues: 234 loop : 0.03 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 1.888 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 244 average time/residue: 2.1414 time to fit residues: 603.6107 Evaluate side-chains 239 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.3216 time to fit residues: 2.7917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 192 optimal weight: 0.4980 chunk 133 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 36168 Z= 0.180 Angle : 0.636 13.970 54205 Z= 0.343 Chirality : 0.037 0.343 6931 Planarity : 0.006 0.129 2832 Dihedral : 12.216 173.532 14289 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1233 helix: 1.77 (0.23), residues: 495 sheet: 0.32 (0.34), residues: 234 loop : 0.11 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 241 time to evaluate : 2.083 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 244 average time/residue: 2.1451 time to fit residues: 603.2224 Evaluate side-chains 237 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 2.090 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 0.3980 chunk 143 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 36168 Z= 0.237 Angle : 0.704 15.037 54205 Z= 0.371 Chirality : 0.039 0.316 6931 Planarity : 0.006 0.132 2832 Dihedral : 12.224 173.383 14289 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1233 helix: 1.65 (0.22), residues: 496 sheet: 0.30 (0.34), residues: 234 loop : 0.09 (0.27), residues: 503 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 2.057 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 241 average time/residue: 2.1869 time to fit residues: 607.5857 Evaluate side-chains 244 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 2.110 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.3480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 180 optimal weight: 0.3980 chunk 75 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 158 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 overall best weight: 3.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 HIS E 146 ASN F 11 HIS L 20 ASN O 35 GLN T 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105446 restraints weight = 27480.395| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 0.47 r_work: 0.3012 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2723 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.109 36168 Z= 0.341 Angle : 0.849 16.601 54205 Z= 0.432 Chirality : 0.044 0.314 6931 Planarity : 0.008 0.137 2832 Dihedral : 12.344 172.509 14289 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.81 (0.23), residues: 1233 helix: 1.34 (0.22), residues: 495 sheet: 0.20 (0.34), residues: 237 loop : 0.02 (0.27), residues: 501 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12301.28 seconds wall clock time: 221 minutes 26.19 seconds (13286.19 seconds total)