Starting phenix.real_space_refine on Sat Dec 16 12:42:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/12_2023/8cgu_16651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/12_2023/8cgu_16651.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/12_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_16651/12_2023/8cgu_16651_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/12_2023/8cgu_16651_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/12_2023/8cgu_16651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/12_2023/8cgu_16651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/12_2023/8cgu_16651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/12_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 20.42, per 1000 atoms: 0.58 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: 22.97 Conformation dependent library (CDL) restraints added in 2.6 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: 25.09 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: 67.47 Time building geometry restraints manager: 23.89 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: 20349 35.74 - 71.49: 1897 71.49 - 107.23: 227 107.23 - 142.97: 6 142.97 - 178.71: 4 Dihedral angle restraints: 22483 sinusoidal: 18852 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 22480 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: 5.790 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: 0.040 Extract box with map and model: 23.510 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 171.490 Find NCS groups from input model: 0.790 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:15.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 217.790 ------------------------------------------------------------------------------- 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 : 21.295 178.715 20137 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP P 60 HIS 0.012 0.003 HIS P 9 PHE 0.030 0.005 PHE O 43 TYR 0.041 0.006 TYR D 76 ARG 0.034 0.004 ARG F 24 *********************** 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 : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 318 average time/residue: 2.1132 time to fit residues: 773.7425 Evaluate side-chains 256 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 2.448 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.3745 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.7959 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 0.043 36168 Z= 0.135 Angle : 0.584 13.090 54205 Z= 0.322 Chirality : 0.035 0.327 6931 Planarity : 0.006 0.120 2832 Dihedral : 21.739 178.794 17646 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.96 % Allowed : 9.14 % Favored : 89.89 % 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: 1.92 (0.23), residues: 493 sheet: 0.13 (0.33), residues: 232 loop : 0.05 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.007 0.001 HIS F 58 PHE 0.018 0.002 PHE O 43 TYR 0.015 0.002 TYR D 51 ARG 0.005 0.001 ARG L 54 *********************** 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: 10 poor density : 261 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 263 average time/residue: 2.1872 time to fit residues: 661.7101 Evaluate side-chains 245 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 2.390 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.3300 time to fit residues: 3.0411 ------------------------------------------------------------------------------- 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: 2.9990 chunk 140 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 223 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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: 0.8017 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 36168 Z= 0.375 Angle : 0.903 16.528 54205 Z= 0.453 Chirality : 0.046 0.332 6931 Planarity : 0.009 0.140 2832 Dihedral : 21.873 175.068 17646 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.44 % Allowed : 10.78 % 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: 0.84 (0.23), residues: 1233 helix: 1.38 (0.22), residues: 499 sheet: 0.15 (0.33), residues: 237 loop : 0.05 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP P 60 HIS 0.010 0.003 HIS P 9 PHE 0.025 0.003 PHE O 43 TYR 0.021 0.004 TYR D 51 ARG 0.015 0.001 ARG L 54 *********************** 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: 15 poor density : 245 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 247 average time/residue: 2.2646 time to fit residues: 644.1367 Evaluate side-chains 245 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.2203 time to fit residues: 5.3855 ------------------------------------------------------------------------------- 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: 5.9990 chunk 155 optimal weight: 0.9990 chunk 107 optimal weight: 0.0040 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 chunk 207 optimal weight: 0.9980 chunk 219 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 F 11 HIS L 20 ASN O 35 GLN O 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36168 Z= 0.125 Angle : 0.549 12.502 54205 Z= 0.304 Chirality : 0.034 0.337 6931 Planarity : 0.005 0.122 2832 Dihedral : 21.676 176.325 17646 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.48 % Allowed : 11.65 % Favored : 87.87 % 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: 1.48 (0.24), residues: 1233 helix: 2.16 (0.23), residues: 493 sheet: 0.31 (0.33), residues: 231 loop : 0.22 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 60 HIS 0.006 0.001 HIS F 58 PHE 0.020 0.001 PHE F 8 TYR 0.011 0.001 TYR D 51 ARG 0.003 0.000 ARG F 91 *********************** 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: 5 poor density : 247 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 249 average time/residue: 2.1192 time to fit residues: 610.1753 Evaluate side-chains 233 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3203 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8019 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 36168 Z= 0.444 Angle : 0.995 17.427 54205 Z= 0.490 Chirality : 0.050 0.324 6931 Planarity : 0.009 0.141 2832 Dihedral : 21.860 172.754 17646 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.96 % Allowed : 11.84 % Favored : 87.20 % 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: 0.74 (0.23), residues: 1233 helix: 1.25 (0.22), residues: 500 sheet: 0.20 (0.33), residues: 237 loop : -0.00 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP P 60 HIS 0.011 0.003 HIS U 56 PHE 0.026 0.003 PHE O 43 TYR 0.024 0.004 TYR D 135 ARG 0.016 0.002 ARG L 54 *********************** 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 251 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 241 time to evaluate : 2.238 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 244 average time/residue: 2.1222 time to fit residues: 596.1600 Evaluate side-chains 239 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 1.3148 time to fit residues: 7.2590 ------------------------------------------------------------------------------- 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: 4.9990 chunk 197 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8000 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36168 Z= 0.248 Angle : 0.728 15.197 54205 Z= 0.381 Chirality : 0.040 0.328 6931 Planarity : 0.007 0.132 2832 Dihedral : 21.789 174.610 17646 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.06 % Allowed : 11.84 % 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: 1.00 (0.23), residues: 1233 helix: 1.56 (0.22), residues: 496 sheet: 0.28 (0.33), residues: 235 loop : 0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 60 HIS 0.008 0.002 HIS P 9 PHE 0.024 0.002 PHE F 8 TYR 0.016 0.003 TYR D 51 ARG 0.012 0.001 ARG L 54 *********************** 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 254 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 243 time to evaluate : 2.458 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 246 average time/residue: 2.0874 time to fit residues: 594.0672 Evaluate side-chains 239 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.4903 time to fit residues: 5.9069 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 184 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 218 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.7994 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36168 Z= 0.216 Angle : 0.682 14.698 54205 Z= 0.363 Chirality : 0.038 0.336 6931 Planarity : 0.007 0.132 2832 Dihedral : 21.789 174.576 17646 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.77 % Allowed : 12.22 % Favored : 87.01 % 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: 1.64 (0.22), residues: 496 sheet: 0.27 (0.33), residues: 235 loop : 0.08 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 60 HIS 0.007 0.002 HIS F 58 PHE 0.023 0.002 PHE F 8 TYR 0.016 0.002 TYR D 51 ARG 0.013 0.001 ARG L 54 *********************** 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 251 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 243 time to evaluate : 2.056 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 247 average time/residue: 2.1907 time to fit residues: 622.9231 Evaluate side-chains 237 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.2215 ------------------------------------------------------------------------------- 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: 0.0030 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 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: 5.9990 chunk 20 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 overall best weight: 1.5790 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36168 Z= 0.200 Angle : 0.663 14.476 54205 Z= 0.355 Chirality : 0.038 0.340 6931 Planarity : 0.007 0.175 2832 Dihedral : 21.783 174.556 17646 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.58 % Allowed : 12.80 % Favored : 86.62 % 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: 1.10 (0.23), residues: 1233 helix: 1.69 (0.22), residues: 496 sheet: 0.31 (0.33), residues: 234 loop : 0.08 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 60 HIS 0.006 0.001 HIS F 58 PHE 0.023 0.002 PHE F 8 TYR 0.016 0.002 TYR D 51 ARG 0.012 0.001 ARG L 54 *********************** 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 244 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 238 time to evaluate : 2.111 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 241 average time/residue: 1.8898 time to fit residues: 524.2632 Evaluate side-chains 241 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.2655 time to fit residues: 2.2127 ------------------------------------------------------------------------------- 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: 0.9990 chunk 191 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: