Starting phenix.real_space_refine on Tue Nov 21 20:38:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/11_2023/8cgu_16651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/11_2023/8cgu_16651.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/11_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_16651/11_2023/8cgu_16651_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/11_2023/8cgu_16651_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/11_2023/8cgu_16651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/11_2023/8cgu_16651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/11_2023/8cgu_16651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/11_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 18.76, per 1000 atoms: 0.53 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: 21.07 Conformation dependent library (CDL) restraints added in 2.5 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: 23.61 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: 70.93 Time building geometry restraints manager: 21.46 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: 18671 35.74 - 71.49: 454 71.49 - 107.23: 37 107.23 - 142.97: 1 142.97 - 178.71: 4 Dihedral angle restraints: 19167 sinusoidal: 15536 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 19164 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: 6.320 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: 23.620 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 167.940 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.940 ------------------------------------------------------------------------------- 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 : 13.345 178.715 16821 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 % Allowed : 3.27 % Favored : 96.34 % 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 : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 318 average time/residue: 2.0243 time to fit residues: 743.1833 Evaluate side-chains 256 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.2296 ------------------------------------------------------------------------------- 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 40 ASN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36168 Z= 0.132 Angle : 0.580 12.895 54205 Z= 0.320 Chirality : 0.035 0.328 6931 Planarity : 0.005 0.124 2832 Dihedral : 12.265 176.478 14330 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.96 % Allowed : 9.34 % Favored : 89.70 % 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: 1.19 (0.23), residues: 1233 helix: 1.93 (0.23), residues: 492 sheet: 0.16 (0.33), residues: 237 loop : 0.06 (0.27), residues: 504 *********************** 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 268 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 260 average time/residue: 2.1443 time to fit residues: 642.7540 Evaluate side-chains 244 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.3773 time to fit residues: 2.7807 ------------------------------------------------------------------------------- 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: 8.9990 chunk 63 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 223 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36168 Z= 0.236 Angle : 0.711 15.154 54205 Z= 0.374 Chirality : 0.039 0.325 6931 Planarity : 0.007 0.133 2832 Dihedral : 12.305 174.237 14330 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.25 % Allowed : 10.59 % Favored : 88.16 % 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: 1.19 (0.23), residues: 1233 helix: 1.82 (0.22), residues: 494 sheet: 0.26 (0.33), residues: 229 loop : 0.12 (0.27), residues: 510 *********************** 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 256 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 2.647 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 244 average time/residue: 2.1434 time to fit residues: 603.7498 Evaluate side-chains 238 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.0876 time to fit residues: 5.1634 ------------------------------------------------------------------------------- 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: 0.6980 chunk 107 optimal weight: 0.0170 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 138 optimal weight: 0.0870 chunk 207 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 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 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36168 Z= 0.128 Angle : 0.554 12.985 54205 Z= 0.307 Chirality : 0.034 0.312 6931 Planarity : 0.005 0.124 2832 Dihedral : 12.170 173.984 14330 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.67 % Allowed : 11.26 % Favored : 88.07 % 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: 1.52 (0.24), residues: 1233 helix: 2.18 (0.23), residues: 493 sheet: 0.32 (0.33), residues: 231 loop : 0.27 (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 252 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 245 time to evaluate : 2.181 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 248 average time/residue: 2.0629 time to fit residues: 592.2655 Evaluate side-chains 232 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.2749 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 187 optimal weight: 0.0870 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36168 Z= 0.264 Angle : 0.743 15.567 54205 Z= 0.386 Chirality : 0.040 0.325 6931 Planarity : 0.007 0.134 2832 Dihedral : 12.309 173.325 14330 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.87 % Allowed : 11.36 % Favored : 87.78 % 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: 1.26 (0.23), residues: 1233 helix: 1.81 (0.22), residues: 494 sheet: 0.38 (0.33), residues: 229 loop : 0.19 (0.27), residues: 510 *********************** 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 250 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 241 time to evaluate : 2.114 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 243 average time/residue: 2.0872 time to fit residues: 587.7686 Evaluate side-chains 238 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 231 time to evaluate : 1.901 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 6 average time/residue: 1.2466 time to fit residues: 11.2479 ------------------------------------------------------------------------------- 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: 6.9990 chunk 197 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 182 optimal weight: 0.0670 chunk 101 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 40 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 36168 Z= 0.381 Angle : 0.908 16.916 54205 Z= 0.455 Chirality : 0.047 0.309 6931 Planarity : 0.008 0.139 2832 Dihedral : 12.463 172.355 14330 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.25 % Allowed : 11.36 % Favored : 87.39 % 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: 0.79 (0.23), residues: 1233 helix: 1.30 (0.22), residues: 494 sheet: 0.27 (0.34), residues: 235 loop : 0.01 (0.27), residues: 504 *********************** 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 251 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 238 time to evaluate : 2.185 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 240 average time/residue: 2.1365 time to fit residues: 593.0926 Evaluate side-chains 236 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 231 time to evaluate : 2.261 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 1.3442 time to fit residues: 7.3583 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 218 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36168 Z= 0.197 Angle : 0.651 14.359 54205 Z= 0.350 Chirality : 0.037 0.319 6931 Planarity : 0.006 0.130 2832 Dihedral : 12.275 173.853 14330 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.67 % Allowed : 11.93 % Favored : 87.39 % 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: 1.15 (0.23), residues: 1233 helix: 1.73 (0.22), residues: 496 sheet: 0.34 (0.33), residues: 234 loop : 0.10 (0.27), residues: 503 *********************** 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 249 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 242 time to evaluate : 1.772 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 244 average time/residue: 1.7120 time to fit residues: 482.1654 Evaluate side-chains 236 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.8261 time to fit residues: 3.4625 ------------------------------------------------------------------------------- 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: 1.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 171 optimal weight: 0.2980 chunk 199 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 T 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36168 Z= 0.266 Angle : 0.745 15.697 54205 Z= 0.389 Chirality : 0.041 0.317 6931 Planarity : 0.007 0.133 2832 Dihedral : 12.333 173.418 14330 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.58 % Allowed : 12.13 % Favored : 87.30 % 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: 1.06 (0.23), residues: 1233 helix: 1.60 (0.22), residues: 494 sheet: 0.34 (0.33), residues: 234 loop : 0.10 (0.27), residues: 505 *********************** 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 241 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 1.996 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 236 average time/residue: 2.0960 time to fit residues: 573.1259 Evaluate side-chains 236 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.5041 time to fit residues: 3.3875 ------------------------------------------------------------------------------- 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: 1.9990 chunk 191 optimal weight: 0.7980 chunk 203 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 184 optimal weight: 0.3980 chunk 192 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 HIS F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 36168 Z= 0.124 Angle : 0.546 12.726 54205 Z= 0.304 Chirality : 0.033 0.317 6931 Planarity : 0.005 0.123 2832 Dihedral : 12.190 173.834 14330 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.38 % Allowed : 12.51 % Favored : 87.10 % 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: 1.44 (0.24), residues: 1233 helix: 2.08 (0.23), residues: 495 sheet: 0.41 (0.34), residues: 229 loop : 0.19 (0.27), residues: 509 *********************** 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 244 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 240 time to evaluate : 2.319 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 242 average time/residue: 2.1589 time to fit residues: 604.2684 Evaluate side-chains 233 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.0788 ------------------------------------------------------------------------------- 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: 0.9980 chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 143 optimal weight: 0.4980 chunk 191 optimal weight: 8.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 T 48 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 36168 Z= 0.355 Angle : 0.865 16.584 54205 Z= 0.437 Chirality : 0.045 0.327 6931 Planarity : 0.008 0.138 2832 Dihedral : 12.430 172.480 14330 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.58 % Allowed : 12.90 % Favored : 86.53 % 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: 0.98 (0.23), residues: 1233 helix: 1.50 (0.22), residues: 494 sheet: 0.31 (0.34), residues: 235 loop : 0.10 (0.27), residues: 504 ********************** 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 241 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 2.045 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 238 average time/residue: 2.1086 time to fit residues: 580.1661 Evaluate side-chains 232 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.3429 time to fit residues: 3.7714 ------------------------------------------------------------------------------- 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: 5.9990 chunk 166 optimal weight: 0.0470 chunk 26 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 180 optimal weight: 0.1980 chunk 75 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 158 optimal weight: 0.0770 chunk 10 optimal weight: 5.9990 overall best weight: 1.4640 ------------------------------------------------------------------------------- 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 20 HIS T 48 GLN T 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108141 restraints weight = 27622.501| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 0.44 r_work: 0.3059 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2773 rms_B_bonded: 4.83 restraints_weight: 0.1250 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 36168 Z= 0.190 Angle : 0.638 14.095 54205 Z= 0.344 Chirality : 0.037 0.317 6931 Planarity : 0.006 0.129 2832 Dihedral : 12.266 173.834 14330 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.48 % Allowed : 13.19 % Favored : 86.33 % 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: 1.19 (0.23), residues: 1233 helix: 1.79 (0.23), residues: 495 sheet: 0.34 (0.33), residues: 234 loop : 0.11 (0.27), residues: 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12294.20 seconds wall clock time: 274 minutes 33.86 seconds (16473.86 seconds total)