Starting phenix.real_space_refine (version: dev) on Tue May 17 17:48:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/05_2022/6nqb_0482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/05_2022/6nqb_0482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/05_2022/6nqb_0482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/05_2022/6nqb_0482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/05_2022/6nqb_0482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/05_2022/6nqb_0482.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "J ARG 45": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 42570 Number of models: 1 Model: "" Number of chains: 17 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: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'CIS': 1, 'TRANS': 91} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "A" Number of atoms: 28767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 28767 Classifications: {'RNA': 1341} Modifications used: {'rna3p_pyr': 512, 'rna2p_pur': 98, 'rna3p_pur': 663, 'rna2p_pyr': 68} Link IDs: {'rna3p': 1175, 'rna2p': 165} Chain breaks: 2 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: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1089 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain breaks: 1 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: "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: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "P" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 629 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "T" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 659 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1696 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.57, per 1000 atoms: 0.58 Number of scatterers: 42570 At special positions: 0 Unit cell: (204.943, 215.673, 154.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 1341 15.00 Mg 1 11.99 O 11781 8.00 N 7902 7.00 C 21496 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: 23.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 18 sheets defined 33.4% alpha, 9.4% beta 250 base pairs and 620 stacking pairs defined. Time for finding SS restraints: 16.46 Creating SS restraints... Processing helix chain 'C' and resid 27 through 40 removed outlier: 4.580A pdb=" N LEU C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.889A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.760A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.796A pdb=" N ILE C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 4.367A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 21 Processing helix chain 'J' and resid 22 through 27 removed outlier: 4.352A pdb=" N GLU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 18 removed outlier: 4.596A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 28 removed outlier: 3.536A pdb=" N LYS N 27 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA N 28 " --> pdb=" O GLU N 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 24 through 28' Processing helix chain 'N' and resid 41 through 49 removed outlier: 3.918A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 removed outlier: 3.867A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 16 Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.851A pdb=" N ILE S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 73 removed outlier: 4.139A pdb=" N GLU S 72 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE S 73 " --> pdb=" O LEU S 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 69 through 73' Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.564A pdb=" N ILE D 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 4.056A pdb=" N VAL D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.738A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.573A pdb=" N ARG D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 157 through 164 removed outlier: 3.619A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.609A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 4.051A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 4.159A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.990A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.835A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 25 removed outlier: 3.588A pdb=" N MET F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.694A pdb=" N GLU F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 71 through 76' Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.745A pdb=" N ARG H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.783A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 36 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 39 " --> pdb=" O ILE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.409A pdb=" N ALA H 115 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.596A pdb=" N LEU L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 9 removed outlier: 3.642A pdb=" N LYS O 9 " --> pdb=" O GLU O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 42 removed outlier: 3.525A pdb=" N ALA O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 73 removed outlier: 3.587A pdb=" N MET O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU O 66 " --> pdb=" O ARG O 62 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR O 68 " --> pdb=" O LYS O 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS O 72 " --> pdb=" O TYR O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 Processing helix chain 'P' and resid 53 through 64 removed outlier: 4.107A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY P 64 " --> pdb=" O TRP P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 removed outlier: 4.322A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 30 removed outlier: 3.557A pdb=" N LEU R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 51 through 60 removed outlier: 3.958A pdb=" N ARG R 56 " --> pdb=" O ARG R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.596A pdb=" N LEU R 64 " --> pdb=" O ALA R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.889A pdb=" N GLN T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN T 20 " --> pdb=" O ALA T 16 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET T 26 " --> pdb=" O SER T 22 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 60 removed outlier: 3.619A pdb=" N PHE T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.725A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 86 removed outlier: 3.904A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 4.320A pdb=" N ASN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.290A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.827A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 removed outlier: 4.019A pdb=" N LYS B 151 " --> pdb=" O GLY B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.592A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 3.511A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 68 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'J' and resid 6 through 12 removed outlier: 3.707A pdb=" N LEU J 10 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR J 69 " --> pdb=" O ARG J 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 66 removed outlier: 3.747A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA7, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AA8, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.967A pdb=" N THR E 36 " --> pdb=" O GLY E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 87 removed outlier: 3.748A pdb=" N LEU E 123 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AB2, first strand: chain 'H' and resid 23 through 24 removed outlier: 3.988A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 100 through 104 removed outlier: 7.386A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU H 123 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.597A pdb=" N GLY L 31 " --> pdb=" O ILE L 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 51 through 55 Processing sheet with id=AB6, first strand: chain 'P' and resid 18 through 21 removed outlier: 4.345A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 7 through 10 removed outlier: 4.025A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG Q 61 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU Q 74 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LYS Q 70 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N HIS Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR Q 41 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE Q 24 " --> pdb=" O THR Q 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.303A pdb=" N GLY B 32 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.165A pdb=" N PHE B 68 " --> pdb=" O VAL B 91 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 594 hydrogen bonds 890 hydrogen bond angles 0 basepair planarities 250 basepair parallelities 620 stacking parallelities Total time for adding SS restraints: 26.71 Time building geometry restraints manager: 24.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5140 1.32 - 1.45: 19614 1.45 - 1.57: 18690 1.57 - 1.69: 2681 1.69 - 1.81: 88 Bond restraints: 46213 Sorted by residual: bond pdb=" C VAL B 46 " pdb=" N PRO B 47 " ideal model delta sigma weight residual 1.335 1.383 -0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" CA ARG R 62 " pdb=" C ARG R 62 " ideal model delta sigma weight residual 1.522 1.569 -0.046 1.37e-02 5.33e+03 1.14e+01 bond pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 1.518 1.629 -0.111 4.01e-02 6.22e+02 7.62e+00 bond pdb=" C SER H 78 " pdb=" N ARG H 79 " ideal model delta sigma weight residual 1.339 1.202 0.137 5.57e-02 3.22e+02 6.09e+00 bond pdb=" CA TYR C 167 " pdb=" CB TYR C 167 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.62e-02 3.81e+03 3.89e+00 ... (remaining 46208 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.35: 6716 105.35 - 112.96: 27245 112.96 - 120.57: 20184 120.57 - 128.18: 12725 128.18 - 135.79: 2182 Bond angle restraints: 69052 Sorted by residual: angle pdb=" C THR B 19 " pdb=" N ARG B 20 " pdb=" CA ARG B 20 " ideal model delta sigma weight residual 120.38 130.91 -10.53 1.37e+00 5.33e-01 5.90e+01 angle pdb=" N ARG Q 5 " pdb=" CA ARG Q 5 " pdb=" C ARG Q 5 " ideal model delta sigma weight residual 114.64 105.31 9.33 1.52e+00 4.33e-01 3.77e+01 angle pdb=" N ALA F 66 " pdb=" CA ALA F 66 " pdb=" C ALA F 66 " ideal model delta sigma weight residual 109.60 116.39 -6.79 1.15e+00 7.56e-01 3.48e+01 angle pdb=" N THR F 26 " pdb=" CA THR F 26 " pdb=" C THR F 26 " ideal model delta sigma weight residual 113.38 106.31 7.07 1.23e+00 6.61e-01 3.30e+01 angle pdb=" N ILE H 6 " pdb=" CA ILE H 6 " pdb=" C ILE H 6 " ideal model delta sigma weight residual 112.96 107.35 5.61 1.00e+00 1.00e+00 3.15e+01 ... (remaining 69047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 23301 35.95 - 71.91: 1324 71.91 - 107.86: 110 107.86 - 143.82: 9 143.82 - 179.77: 11 Dihedral angle restraints: 24755 sinusoidal: 19726 harmonic: 5029 Sorted by residual: 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 65.79 134.21 1 1.50e+01 4.44e-03 7.24e+01 dihedral pdb=" O4' U A 85 " pdb=" C1' U A 85 " pdb=" N1 U A 85 " pdb=" C2 U A 85 " ideal model delta sinusoidal sigma weight residual 232.00 52.23 179.77 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A1322 " pdb=" C1' C A1322 " pdb=" N1 C A1322 " pdb=" C2 C A1322 " ideal model delta sinusoidal sigma weight residual -128.00 48.56 -176.56 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 24752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7983 0.075 - 0.151: 765 0.151 - 0.226: 58 0.226 - 0.301: 9 0.301 - 0.377: 9 Chirality restraints: 8824 Sorted by residual: chirality pdb=" C1' U A 365 " pdb=" O4' U A 365 " pdb=" C2' U A 365 " pdb=" N1 U A 365 " both_signs ideal model delta sigma weight residual False 2.47 2.09 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE Q 54 " pdb=" CA ILE Q 54 " pdb=" CG1 ILE Q 54 " pdb=" CG2 ILE Q 54 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C3' C A 372 " pdb=" C4' C A 372 " pdb=" O3' C A 372 " pdb=" C2' C A 372 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 8821 not shown) Planarity restraints: 3762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 23 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 24 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 24 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 24 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS L 26 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.78e+00 pdb=" N PRO L 27 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 27 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 27 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN P 40 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO P 41 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO P 41 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO P 41 " -0.038 5.00e-02 4.00e+02 ... (remaining 3759 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 7047 2.75 - 3.29: 37901 3.29 - 3.83: 89123 3.83 - 4.36: 101178 4.36 - 4.90: 137572 Nonbonded interactions: 372821 Sorted by model distance: nonbonded pdb=" O2' U A 662 " pdb=" OP1 G A 836 " model vdw 2.216 2.440 nonbonded pdb=" O SER N 99 " pdb=" O2' C A1114 " model vdw 2.227 2.440 nonbonded pdb=" O2' U A 343 " pdb=" O6 G A 346 " model vdw 2.239 2.440 nonbonded pdb=" OP2 C A 522 " pdb=" OH TYR L 65 " model vdw 2.260 2.440 nonbonded pdb=" OP1 U A 62 " pdb=" O2' C A 385 " model vdw 2.263 2.440 ... (remaining 372816 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1341 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 21496 2.51 5 N 7902 2.21 5 O 11781 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 1.340 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: 9.720 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.350 Process input model: 129.640 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.137 46213 Z= 0.340 Angle : 0.981 18.166 69052 Z= 0.501 Chirality : 0.047 0.377 8824 Planarity : 0.006 0.080 3762 Dihedral : 17.600 179.773 21499 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.64 % Favored : 86.31 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -5.36 (0.15), residues: 1716 helix: -4.19 (0.12), residues: 487 sheet: -3.39 (0.28), residues: 231 loop : -3.37 (0.16), residues: 998 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 542 time to evaluate : 2.600 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 545 average time/residue: 0.6438 time to fit residues: 538.0079 Evaluate side-chains 303 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 2.401 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3480 time to fit residues: 3.3447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 4.9990 chunk 226 optimal weight: 0.0000 chunk 125 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 chunk 121 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 40.0000 chunk 174 optimal weight: 30.0000 chunk 271 optimal weight: 0.1980 overall best weight: 3.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS C 24 ASN C 175 HIS N 59 GLN D 99 ASN D 119 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN F 55 HIS F 63 ASN H 15 ASN H 17 GLN H 37 ASN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS B 121 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 46213 Z= 0.225 Angle : 0.717 14.276 69052 Z= 0.370 Chirality : 0.040 0.292 8824 Planarity : 0.006 0.130 3762 Dihedral : 18.047 179.820 18024 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.82 % Favored : 87.06 % Rotamer Outliers : 4.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.49 (0.17), residues: 1716 helix: -2.88 (0.18), residues: 516 sheet: -3.15 (0.30), residues: 238 loop : -3.06 (0.18), residues: 962 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 361 time to evaluate : 2.781 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 34 residues processed: 397 average time/residue: 0.5742 time to fit residues: 365.9452 Evaluate side-chains 332 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 298 time to evaluate : 2.712 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3993 time to fit residues: 28.2638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 225 optimal weight: 0.3980 chunk 184 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 269 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN N 59 GLN D 139 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS H 37 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN O 37 HIS P 26 ASN T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS B 38 HIS B 121 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 46213 Z= 0.282 Angle : 0.743 12.965 69052 Z= 0.380 Chirality : 0.041 0.300 8824 Planarity : 0.006 0.091 3762 Dihedral : 18.152 179.762 18024 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.33 % Favored : 84.62 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.95 (0.18), residues: 1716 helix: -2.20 (0.20), residues: 524 sheet: -2.73 (0.33), residues: 216 loop : -2.92 (0.18), residues: 976 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 320 time to evaluate : 2.636 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 28 residues processed: 356 average time/residue: 0.5732 time to fit residues: 329.1424 Evaluate side-chains 289 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 261 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3986 time to fit residues: 23.2238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 chunk 141 optimal weight: 40.0000 chunk 30 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 142 optimal weight: 50.0000 chunk 258 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN D 35 GLN D 73 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN L 4 ASN L 5 GLN ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.134 46213 Z= 0.428 Angle : 0.879 13.262 69052 Z= 0.445 Chirality : 0.047 0.338 8824 Planarity : 0.006 0.088 3762 Dihedral : 18.615 178.810 18024 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.43 % Favored : 83.51 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.97 (0.18), residues: 1716 helix: -2.22 (0.20), residues: 529 sheet: -2.94 (0.32), residues: 222 loop : -2.87 (0.19), residues: 965 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 272 time to evaluate : 2.661 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 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 revert: symmetry clash outliers start: 66 outliers final: 39 residues processed: 313 average time/residue: 0.5792 time to fit residues: 297.7426 Evaluate side-chains 286 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 247 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3900 time to fit residues: 31.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 0.7980 chunk 164 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 246 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS D 135 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN L 5 GLN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 46213 Z= 0.294 Angle : 0.733 12.545 69052 Z= 0.377 Chirality : 0.042 0.313 8824 Planarity : 0.005 0.100 3762 Dihedral : 18.205 180.000 18024 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.79 % Favored : 84.15 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.59 (0.19), residues: 1716 helix: -1.81 (0.22), residues: 526 sheet: -2.66 (0.33), residues: 220 loop : -2.73 (0.19), residues: 970 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 277 time to evaluate : 2.609 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 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: 44 outliers final: 27 residues processed: 306 average time/residue: 0.5670 time to fit residues: 283.0519 Evaluate side-chains 277 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 250 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4363 time to fit residues: 24.0328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 10.0000 chunk 260 optimal weight: 0.0470 chunk 57 optimal weight: 7.9990 chunk 169 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 240 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 151 optimal weight: 40.0000 overall best weight: 5.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS D 135 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN L 5 GLN ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 46213 Z= 0.319 Angle : 0.760 12.890 69052 Z= 0.388 Chirality : 0.042 0.324 8824 Planarity : 0.005 0.084 3762 Dihedral : 18.246 179.487 18024 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.14 % Favored : 83.80 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.62 (0.19), residues: 1716 helix: -1.82 (0.21), residues: 530 sheet: -2.75 (0.32), residues: 235 loop : -2.72 (0.19), residues: 951 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 262 time to evaluate : 2.777 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 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: 52 outliers final: 29 residues processed: 295 average time/residue: 0.5487 time to fit residues: 260.9095 Evaluate side-chains 277 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 2.388 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3843 time to fit residues: 22.9672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 164 optimal weight: 30.0000 chunk 211 optimal weight: 7.9990 chunk 163 optimal weight: 40.0000 chunk 243 optimal weight: 5.9990 chunk 161 optimal weight: 50.0000 chunk 288 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 175 optimal weight: 30.0000 chunk 133 optimal weight: 20.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN L 5 GLN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 46213 Z= 0.226 Angle : 0.667 12.144 69052 Z= 0.344 Chirality : 0.038 0.326 8824 Planarity : 0.005 0.077 3762 Dihedral : 17.836 179.634 18024 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.86 % Favored : 85.08 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.32 (0.20), residues: 1716 helix: -1.50 (0.22), residues: 535 sheet: -2.58 (0.32), residues: 243 loop : -2.57 (0.20), residues: 938 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 287 time to evaluate : 2.772 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 297 average time/residue: 0.5838 time to fit residues: 280.9064 Evaluate side-chains 267 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 255 time to evaluate : 2.577 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4727 time to fit residues: 12.6320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 172 optimal weight: 40.0000 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 142 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 GLN T 51 ASN T 60 GLN B 93 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.977 46213 Z= 0.516 Angle : 0.899 106.097 69052 Z= 0.426 Chirality : 0.043 0.362 8824 Planarity : 0.006 0.160 3762 Dihedral : 17.885 179.517 18024 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.03 % Favored : 84.91 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.39 (0.19), residues: 1716 helix: -1.55 (0.22), residues: 533 sheet: -2.67 (0.32), residues: 245 loop : -2.60 (0.20), residues: 938 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 263 time to evaluate : 2.401 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 27 residues processed: 283 average time/residue: 0.5683 time to fit residues: 261.4755 Evaluate side-chains 277 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 250 time to evaluate : 2.913 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4548 time to fit residues: 24.9451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 3.9990 chunk 276 optimal weight: 0.9990 chunk 251 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 161 optimal weight: 50.0000 chunk 116 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 242 optimal weight: 0.7980 chunk 253 optimal weight: 0.9980 chunk 267 optimal weight: 0.0020 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN L 5 GLN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.977 46213 Z= 0.557 Angle : 0.923 106.100 69052 Z= 0.443 Chirality : 0.043 0.361 8824 Planarity : 0.009 0.269 3762 Dihedral : 17.885 179.517 18024 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 28.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.03 % Favored : 84.91 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.39 (0.19), residues: 1716 helix: -1.55 (0.22), residues: 533 sheet: -2.67 (0.32), residues: 245 loop : -2.60 (0.20), residues: 938 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 250 time to evaluate : 2.743 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 251 average time/residue: 0.5987 time to fit residues: 243.3894 Evaluate side-chains 250 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 2.587 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3697 time to fit residues: 4.2831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 30.0000 chunk 283 optimal weight: 6.9990 chunk 173 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 197 optimal weight: 0.1980 chunk 297 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 24 optimal weight: 0.0370 chunk 183 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 overall best weight: 3.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.977 46213 Z= 0.557 Angle : 0.923 106.100 69052 Z= 0.443 Chirality : 0.043 0.361 8824 Planarity : 0.009 0.269 3762 Dihedral : 17.885 179.517 18024 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 28.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.03 % Favored : 84.91 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.39 (0.19), residues: 1716 helix: -1.55 (0.22), residues: 533 sheet: -2.67 (0.32), residues: 245 loop : -2.60 (0.20), residues: 938 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 2.751 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.5868 time to fit residues: 237.5803 Evaluate side-chains 250 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3971 time to fit residues: 3.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 237 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.100579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.076369 restraints weight = 197431.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.078245 restraints weight = 75607.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.078650 restraints weight = 41245.016| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.977 46213 Z= 0.557 Angle : 0.923 106.100 69052 Z= 0.443 Chirality : 0.043 0.361 8824 Planarity : 0.009 0.269 3762 Dihedral : 17.885 179.517 18024 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.03 % Favored : 84.91 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.39 (0.19), residues: 1716 helix: -1.55 (0.22), residues: 533 sheet: -2.67 (0.32), residues: 245 loop : -2.60 (0.20), residues: 938 =============================================================================== Job complete usr+sys time: 6436.98 seconds wall clock time: 120 minutes 44.82 seconds (7244.82 seconds total)