Starting phenix.real_space_refine on Sat Dec 9 08:40:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/12_2023/8eyq_28692_updated.pdb" } resolution = 3.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14664 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1525 5.49 5 S 54 5.16 5 C 24261 2.51 5 N 8995 2.21 5 O 13355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "O ARG 72": "NH1" <-> "NH2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ARG 78": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 48190 Number of models: 1 Model: "" Number of chains: 18 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: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} 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: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} 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: "A" Number of atoms: 32722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1525, 32722 Classifications: {'RNA': 1525} Modifications used: {'rna2p_pur': 123, 'rna2p_pyr': 93, 'rna3p': 1, 'rna3p_pur': 745, 'rna3p_pyr': 563} Link IDs: {'rna2p': 215, 'rna3p': 1309} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 651 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Time building chain proxies: 18.90, per 1000 atoms: 0.39 Number of scatterers: 48190 At special positions: 0 Unit cell: (212.04, 172.71, 224.865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 1525 15.00 O 13355 8.00 N 8995 7.00 C 24261 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=0, symmetry=0 Time building additional restraints: 20.09 Conformation dependent library (CDL) restraints added in 2.3 seconds 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 21 sheets defined 35.4% alpha, 15.3% beta 486 base pairs and 759 stacking pairs defined. Time for finding SS restraints: 19.70 Creating SS restraints... Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.832A pdb=" N GLN D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) 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 104 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.569A pdb=" N LEU D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.685A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 12 through 31 removed outlier: 4.704A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 18 " --> pdb=" O SER F 15 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 5.023A pdb=" N ILE F 22 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 26 " --> pdb=" O GLU F 23 " (cutoff:3.500A) 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 43 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 47 through 50 removed outlier: 3.927A pdb=" N SER K 50 " --> pdb=" O ALA K 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 47 through 50' Processing helix chain 'K' and resid 54 through 58 Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.671A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 102 removed outlier: 4.587A pdb=" N ILE K 97 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU K 100 " --> pdb=" O ILE K 97 " (cutoff:3.500A) 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 14 Processing helix chain 'O' and resid 27 through 45 removed outlier: 3.915A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA O 44 " --> pdb=" O GLN O 40 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 72 removed outlier: 4.220A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG O 64 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 84 Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.735A pdb=" N VAL P 61 " --> pdb=" O ILE P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 30 through 32 No H-bonds generated for 'chain 'R' and resid 30 through 32' 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 65 removed outlier: 3.670A pdb=" N ALA R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 41 removed outlier: 4.589A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA T 17 " --> pdb=" O GLN T 13 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG T 18 " --> pdb=" O SER T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 removed outlier: 3.645A pdb=" N THR T 80 " --> pdb=" O LYS T 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.680A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 48 removed outlier: 3.597A pdb=" N MET I 46 " --> pdb=" O GLU I 42 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL I 47 " --> pdb=" O THR I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 72 through 91 removed outlier: 3.696A pdb=" N ASP I 91 " --> pdb=" O LEU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 31 removed outlier: 4.763A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 removed outlier: 4.136A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 removed outlier: 3.633A pdb=" N LEU M 19 " --> pdb=" O ALA M 15 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 15 through 20' Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 3.657A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 83 Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 20 removed outlier: 3.849A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 33 Processing helix chain 'N' and resid 40 through 50 removed outlier: 4.137A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 81 through 90 Processing helix chain 'S' and resid 13 through 24 removed outlier: 3.815A pdb=" N LYS S 17 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 71 through 73 No H-bonds generated for 'chain 'S' and resid 71 through 73' Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.571A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 48 through 53 removed outlier: 3.721A pdb=" N GLY E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.440A 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 88 Processing sheet with id= D, first strand: chain 'F' and resid 38 through 41 removed outlier: 4.303A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.628A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.882A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 106 through 112 removed outlier: 3.536A pdb=" N LEU K 82 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.875A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'P' and resid 3 through 5 Processing sheet with id= J, first strand: chain 'P' and resid 8 through 11 Processing sheet with id= K, first strand: chain 'Q' and resid 43 through 47 removed outlier: 3.648A pdb=" N SER Q 14 " --> pdb=" O VAL Q 22 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Q' and resid 27 through 30 Processing sheet with id= M, first strand: chain 'Q' and resid 61 through 63 Processing sheet with id= N, first strand: chain 'Q' and resid 58 through 60 removed outlier: 3.820A pdb=" N VAL Q 58 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU Q 80 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 99 through 105 removed outlier: 6.503A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.587A pdb=" N GLU C 166 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 187 through 190 Processing sheet with id= R, first strand: chain 'I' and resid 5 through 12 removed outlier: 4.116A pdb=" N ARG I 12 " --> pdb=" O SER I 15 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR I 64 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS I 22 " --> pdb=" O ASP I 62 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP I 62 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 70 through 76 removed outlier: 3.506A pdb=" N VAL J 74 " --> pdb=" O ILE J 8 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 45 through 52 removed outlier: 3.548A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR J 65 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 48 through 52 551 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1212 hydrogen bonds 1892 hydrogen bond angles 0 basepair planarities 486 basepair parallelities 759 stacking parallelities Total time for adding SS restraints: 36.82 Time building geometry restraints manager: 21.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4704 1.31 - 1.44: 23061 1.44 - 1.56: 21420 1.56 - 1.69: 3048 1.69 - 1.81: 95 Bond restraints: 52328 Sorted by residual: bond pdb=" N3 2MG A1207 " pdb=" C4 2MG A1207 " ideal model delta sigma weight residual 1.496 1.337 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" C2 2MG A1207 " pdb=" N3 2MG A1207 " ideal model delta sigma weight residual 1.465 1.308 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C2 2MG A1207 " pdb=" N2 2MG A1207 " ideal model delta sigma weight residual 1.475 1.329 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" C5 2MG A1207 " pdb=" C6 2MG A1207 " ideal model delta sigma weight residual 1.538 1.416 0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" CA GLN H 4 " pdb=" C GLN H 4 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.28e-02 6.10e+03 3.73e+01 ... (remaining 52323 not shown) Histogram of bond angle deviations from ideal: 95.27 - 103.14: 3242 103.14 - 111.01: 27870 111.01 - 118.88: 20465 118.88 - 126.75: 22485 126.75 - 134.61: 4148 Bond angle restraints: 78210 Sorted by residual: angle pdb=" O3' C A 930 " pdb=" P C A 931 " pdb=" O5' C A 931 " ideal model delta sigma weight residual 104.00 118.95 -14.95 1.50e+00 4.44e-01 9.93e+01 angle pdb=" O3' G A 925 " pdb=" C3' G A 925 " pdb=" C2' G A 925 " ideal model delta sigma weight residual 109.50 123.85 -14.35 1.50e+00 4.44e-01 9.15e+01 angle pdb=" N GLY H 68 " pdb=" CA GLY H 68 " pdb=" C GLY H 68 " ideal model delta sigma weight residual 115.08 100.95 14.13 1.64e+00 3.72e-01 7.42e+01 angle pdb=" N PHE C 130 " pdb=" CA PHE C 130 " pdb=" C PHE C 130 " ideal model delta sigma weight residual 111.71 120.22 -8.51 1.15e+00 7.56e-01 5.48e+01 angle pdb=" N HIS K 24 " pdb=" CA HIS K 24 " pdb=" C HIS K 24 " ideal model delta sigma weight residual 109.96 99.66 10.30 1.50e+00 4.44e-01 4.71e+01 ... (remaining 78205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 29063 35.98 - 71.97: 2858 71.97 - 107.95: 369 107.95 - 143.94: 13 143.94 - 179.92: 13 Dihedral angle restraints: 32316 sinusoidal: 26690 harmonic: 5626 Sorted by residual: dihedral pdb=" O4' C A1028 " pdb=" C1' C A1028 " pdb=" N1 C A1028 " pdb=" C2 C A1028 " ideal model delta sinusoidal sigma weight residual 200.00 37.05 162.95 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U A1008 " pdb=" C1' U A1008 " pdb=" N1 U A1008 " pdb=" C2 U A1008 " ideal model delta sinusoidal sigma weight residual 200.00 39.84 160.16 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U A1030 " pdb=" C1' U A1030 " pdb=" N1 U A1030 " pdb=" C2 U A1030 " ideal model delta sinusoidal sigma weight residual 200.00 44.80 155.20 1 1.50e+01 4.44e-03 8.14e+01 ... (remaining 32313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 9897 0.179 - 0.358: 71 0.358 - 0.537: 3 0.537 - 0.716: 1 0.716 - 0.895: 1 Chirality restraints: 9973 Sorted by residual: chirality pdb=" C3' G A 925 " pdb=" C4' G A 925 " pdb=" O3' G A 925 " pdb=" C2' G A 925 " both_signs ideal model delta sigma weight residual False -2.74 -1.85 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C3' G A1392 " pdb=" C4' G A1392 " pdb=" O3' G A1392 " pdb=" C2' G A1392 " both_signs ideal model delta sigma weight residual False -2.48 -1.87 -0.61 2.00e-01 2.50e+01 9.37e+00 chirality pdb=" C4' G A1392 " pdb=" C5' G A1392 " pdb=" O4' G A1392 " pdb=" C3' G A1392 " both_signs ideal model delta sigma weight residual False -2.50 -2.01 -0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 9970 not shown) Planarity restraints: 4251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " 0.016 2.00e-02 2.50e+03 5.55e-01 6.93e+03 pdb=" C4' 2MG A1207 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " 0.625 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " -0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " -0.530 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " -0.226 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " 0.876 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " 0.233 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " -0.835 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 876 " -0.034 2.00e-02 2.50e+03 3.64e-02 2.98e+01 pdb=" N1 C A 876 " 0.086 2.00e-02 2.50e+03 pdb=" C2 C A 876 " -0.054 2.00e-02 2.50e+03 pdb=" O2 C A 876 " 0.013 2.00e-02 2.50e+03 pdb=" N3 C A 876 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C A 876 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C A 876 " -0.000 2.00e-02 2.50e+03 pdb=" C5 C A 876 " -0.010 2.00e-02 2.50e+03 pdb=" C6 C A 876 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 854 " 0.028 2.00e-02 2.50e+03 3.53e-02 2.80e+01 pdb=" N1 U A 854 " -0.082 2.00e-02 2.50e+03 pdb=" C2 U A 854 " 0.056 2.00e-02 2.50e+03 pdb=" O2 U A 854 " -0.014 2.00e-02 2.50e+03 pdb=" N3 U A 854 " -0.008 2.00e-02 2.50e+03 pdb=" C4 U A 854 " 0.000 2.00e-02 2.50e+03 pdb=" O4 U A 854 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U A 854 " 0.010 2.00e-02 2.50e+03 pdb=" C6 U A 854 " 0.012 2.00e-02 2.50e+03 ... (remaining 4248 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 21 2.15 - 2.84: 14604 2.84 - 3.52: 67963 3.52 - 4.21: 139862 4.21 - 4.90: 191810 Nonbonded interactions: 414260 Sorted by model distance: nonbonded pdb=" O6 G A 927 " pdb=" O2 U A1390 " model vdw 1.460 2.432 nonbonded pdb=" C6 U A 789 " pdb=" O2' G A 791 " model vdw 1.584 3.340 nonbonded pdb=" N3 U A 789 " pdb=" N7 A A 792 " model vdw 1.683 2.600 nonbonded pdb=" O4 U A 789 " pdb=" N3 G A 791 " model vdw 1.715 3.120 nonbonded pdb=" C5 U A 789 " pdb=" C1' G A 791 " model vdw 1.872 3.770 ... (remaining 414255 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: 0.010 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.030 Extract box with map and model: 12.400 Check model and map are aligned: 0.540 Set scattering table: 0.350 Process input model: 129.630 Find NCS groups from input model: 0.760 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 52328 Z= 0.335 Angle : 0.816 17.128 78210 Z= 0.465 Chirality : 0.048 0.895 9973 Planarity : 0.011 0.555 4251 Dihedral : 22.231 179.923 28684 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.94 % Favored : 92.49 % Rotamer: Outliers : 1.29 % Allowed : 25.37 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.18), residues: 1931 helix: -0.84 (0.19), residues: 670 sheet: -0.83 (0.27), residues: 350 loop : -1.95 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP S 34 HIS 0.019 0.001 HIS F 3 PHE 0.030 0.002 PHE C 130 TYR 0.036 0.002 TYR O 78 ARG 0.016 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 461 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 5 residues processed: 475 average time/residue: 0.5539 time to fit residues: 412.3333 Evaluate side-chains 340 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 335 time to evaluate : 2.063 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3296 time to fit residues: 5.4515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.8980 chunk 257 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 GLN F 3 HIS F 17 GLN H 118 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN T 70 ASN T 82 GLN I 32 GLN S 56 GLN S 57 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 52328 Z= 0.359 Angle : 0.717 13.821 78210 Z= 0.368 Chirality : 0.040 0.308 9973 Planarity : 0.006 0.122 4251 Dihedral : 22.311 179.059 24773 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 4.80 % Allowed : 21.49 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 1931 helix: 0.01 (0.20), residues: 678 sheet: -0.55 (0.27), residues: 359 loop : -1.44 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 201 HIS 0.009 0.002 HIS O 51 PHE 0.018 0.002 PHE H 66 TYR 0.023 0.002 TYR L 117 ARG 0.013 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 333 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 48 residues processed: 386 average time/residue: 0.5185 time to fit residues: 326.0470 Evaluate side-chains 350 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 302 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3504 time to fit residues: 34.1105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 334 optimal weight: 30.0000 chunk 275 optimal weight: 6.9990 chunk 306 optimal weight: 7.9990 chunk 105 optimal weight: 0.4980 chunk 248 optimal weight: 30.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS K 81 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 52328 Z= 0.315 Angle : 0.647 12.323 78210 Z= 0.335 Chirality : 0.038 0.267 9973 Planarity : 0.005 0.118 4251 Dihedral : 22.262 179.556 24773 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 3.33 % Allowed : 22.84 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1931 helix: 0.38 (0.20), residues: 680 sheet: -0.45 (0.27), residues: 368 loop : -1.21 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 201 HIS 0.012 0.001 HIS O 38 PHE 0.014 0.002 PHE D 182 TYR 0.018 0.002 TYR M 23 ARG 0.006 0.001 ARG P 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 332 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 31 residues processed: 368 average time/residue: 0.5042 time to fit residues: 305.6544 Evaluate side-chains 340 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 309 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3872 time to fit residues: 24.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 7.9990 chunk 232 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 chunk 328 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 294 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 52328 Z= 0.206 Angle : 0.566 12.003 78210 Z= 0.296 Chirality : 0.034 0.267 9973 Planarity : 0.005 0.116 4251 Dihedral : 22.120 179.946 24773 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 2.65 % Allowed : 23.03 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1931 helix: 0.69 (0.20), residues: 683 sheet: -0.24 (0.27), residues: 375 loop : -1.03 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.005 0.001 HIS S 52 PHE 0.012 0.001 PHE E 31 TYR 0.023 0.002 TYR M 23 ARG 0.005 0.001 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 334 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 358 average time/residue: 0.4936 time to fit residues: 290.2050 Evaluate side-chains 336 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 316 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3313 time to fit residues: 14.9135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 244 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 280 optimal weight: 30.0000 chunk 227 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 135 ASN K 24 HIS K 64 GLN O 38 HIS P 59 HIS I 81 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 52328 Z= 0.474 Angle : 0.744 12.289 78210 Z= 0.378 Chirality : 0.043 0.272 9973 Planarity : 0.006 0.116 4251 Dihedral : 22.341 179.983 24773 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.51 % Rotamer: Outliers : 3.02 % Allowed : 25.74 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1931 helix: 0.31 (0.20), residues: 678 sheet: -0.44 (0.27), residues: 368 loop : -1.23 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.007 0.001 HIS O 51 PHE 0.019 0.002 PHE H 66 TYR 0.020 0.002 TYR M 23 ARG 0.009 0.001 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 319 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 25 residues processed: 351 average time/residue: 0.4911 time to fit residues: 285.0116 Evaluate side-chains 334 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 309 time to evaluate : 2.067 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3513 time to fit residues: 18.6818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 24 HIS K 64 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 52328 Z= 0.193 Angle : 0.571 11.994 78210 Z= 0.299 Chirality : 0.034 0.280 9973 Planarity : 0.005 0.115 4251 Dihedral : 22.144 179.986 24773 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 1.91 % Allowed : 26.66 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 1931 helix: 0.58 (0.20), residues: 683 sheet: -0.30 (0.27), residues: 377 loop : -1.04 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.004 0.001 HIS O 42 PHE 0.033 0.001 PHE N 73 TYR 0.020 0.002 TYR M 23 ARG 0.005 0.000 ARG M 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 327 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 344 average time/residue: 0.5159 time to fit residues: 291.4094 Evaluate side-chains 336 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 321 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3440 time to fit residues: 12.1719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 chunk 187 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 276 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 overall best weight: 5.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 52328 Z= 0.331 Angle : 0.662 12.205 78210 Z= 0.342 Chirality : 0.039 0.272 9973 Planarity : 0.005 0.116 4251 Dihedral : 22.254 179.442 24773 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer: Outliers : 1.72 % Allowed : 28.02 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1931 helix: 0.38 (0.20), residues: 684 sheet: -0.43 (0.27), residues: 370 loop : -1.08 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 201 HIS 0.006 0.001 HIS O 38 PHE 0.017 0.002 PHE N 21 TYR 0.020 0.002 TYR M 23 ARG 0.006 0.001 ARG S 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 323 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 335 average time/residue: 0.5110 time to fit residues: 280.7413 Evaluate side-chains 330 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 314 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3463 time to fit residues: 12.7650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 257 optimal weight: 30.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 52328 Z= 0.374 Angle : 0.690 12.100 78210 Z= 0.356 Chirality : 0.040 0.268 9973 Planarity : 0.006 0.115 4251 Dihedral : 22.314 179.546 24773 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 1.72 % Allowed : 27.46 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1931 helix: 0.27 (0.20), residues: 675 sheet: -0.53 (0.28), residues: 366 loop : -1.06 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 201 HIS 0.007 0.001 HIS O 51 PHE 0.019 0.002 PHE N 21 TYR 0.021 0.002 TYR M 23 ARG 0.006 0.001 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 312 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 328 average time/residue: 0.4995 time to fit residues: 269.9227 Evaluate side-chains 322 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 305 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3573 time to fit residues: 13.6044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 286 optimal weight: 0.0670 chunk 305 optimal weight: 0.0970 chunk 183 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 239 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 overall best weight: 3.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 GLN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS P 63 GLN C 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 52328 Z= 0.239 Angle : 0.603 12.012 78210 Z= 0.314 Chirality : 0.036 0.287 9973 Planarity : 0.005 0.115 4251 Dihedral : 22.192 179.275 24773 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 0.92 % Allowed : 28.39 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 1931 helix: 0.48 (0.20), residues: 676 sheet: -0.50 (0.27), residues: 381 loop : -0.93 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.004 0.001 HIS S 52 PHE 0.018 0.001 PHE S 61 TYR 0.019 0.002 TYR M 23 ARG 0.006 0.000 ARG S 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 314 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 325 average time/residue: 0.5154 time to fit residues: 275.4374 Evaluate side-chains 315 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 306 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3626 time to fit residues: 8.3693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 338 optimal weight: 4.9990 chunk 311 optimal weight: 0.0050 chunk 269 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 52328 Z= 0.308 Angle : 0.648 12.098 78210 Z= 0.336 Chirality : 0.038 0.280 9973 Planarity : 0.005 0.116 4251 Dihedral : 22.241 178.792 24773 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.51 % Rotamer: Outliers : 0.49 % Allowed : 28.82 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1931 helix: 0.41 (0.20), residues: 672 sheet: -0.49 (0.27), residues: 375 loop : -0.95 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.005 0.001 HIS O 51 PHE 0.019 0.002 PHE N 21 TYR 0.020 0.002 TYR M 23 ARG 0.006 0.001 ARG S 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 304 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 307 average time/residue: 0.4958 time to fit residues: 252.3159 Evaluate side-chains 309 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 303 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4121 time to fit residues: 6.6586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 277 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 GLN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.088384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.059712 restraints weight = 162485.328| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.55 r_work: 0.2858 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 52328 Z= 0.231 Angle : 0.594 12.001 78210 Z= 0.309 Chirality : 0.035 0.290 9973 Planarity : 0.005 0.115 4251 Dihedral : 22.170 178.506 24773 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 0.43 % Allowed : 29.31 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 1931 helix: 0.56 (0.20), residues: 670 sheet: -0.49 (0.27), residues: 376 loop : -0.85 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.005 0.001 HIS O 38 PHE 0.032 0.002 PHE N 73 TYR 0.021 0.002 TYR M 23 ARG 0.005 0.000 ARG S 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8289.97 seconds wall clock time: 147 minutes 47.96 seconds (8867.96 seconds total)