Starting phenix.real_space_refine (version: dev) on Fri Apr 8 07:50:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/04_2022/6yt9_10914.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/04_2022/6yt9_10914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/04_2022/6yt9_10914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/04_2022/6yt9_10914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/04_2022/6yt9_10914.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/04_2022/6yt9_10914.pdb" } resolution = 2.7 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= 0.008 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 None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 33279 Number of models: 1 Model: "" Number of chains: 17 Chain: "2" Number of atoms: 19228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 19228 Classifications: {'RNA': 894} Modifications used: {'rna3p_pyr': 326, 'rna2p_pur': 73, 'rna3p_pur': 456, 'rna2p_pyr': 39} Link IDs: {'rna3p': 781, 'rna2p': 112} Chain breaks: 3 Chain: "4" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3129 Classifications: {'RNA': 146} Modifications used: {'rna3p_pyr': 59, 'rna2p_pur': 8, 'rna3p_pur': 73, 'rna2p_pyr': 6} Link IDs: {'rna3p': 131, 'rna2p': 14} Chain: "c" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1079 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 7, 'TRANS': 211} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 669 Unresolved non-hydrogen angles: 854 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 372 Chain: "e" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1592 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 200} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "f" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "g" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 858 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "i" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "l" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 836 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "p" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "r" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "s" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 434 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "u" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "v" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 389 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "2" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "4" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 17.66, per 1000 atoms: 0.53 Number of scatterers: 33279 At special positions: 0 Unit cell: (167.205, 188.505, 174.66, 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 28 16.00 P 1040 15.00 Mg 56 11.99 O 9213 8.00 N 6236 7.00 C 16706 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: 16.32 Conformation dependent library (CDL) restraints added in 2.0 seconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 41.3% alpha, 19.1% beta 368 base pairs and 597 stacking pairs defined. Time for finding SS restraints: 15.75 Creating SS restraints... Processing helix chain 'c' and resid 11 through 15 removed outlier: 3.823A pdb=" N GLY c 15 " --> pdb=" O LEU c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 30 removed outlier: 3.644A pdb=" N ARG c 30 " --> pdb=" O PRO c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 65 removed outlier: 3.981A pdb=" N ASP c 54 " --> pdb=" O PRO c 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 78 through 88 removed outlier: 3.894A pdb=" N ARG c 83 " --> pdb=" O SER c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 120 removed outlier: 3.699A pdb=" N GLN c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER c 112 " --> pdb=" O THR c 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG c 115 " --> pdb=" O GLN c 111 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 removed outlier: 3.710A pdb=" N GLN c 124 " --> pdb=" O GLN c 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP c 125 " --> pdb=" O THR c 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 120 through 125' Processing helix chain 'c' and resid 135 through 151 removed outlier: 4.303A pdb=" N ARG c 139 " --> pdb=" O GLU c 135 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER c 149 " --> pdb=" O LYS c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 181 Processing helix chain 'c' and resid 208 through 224 Processing helix chain 'e' and resid 8 through 16 removed outlier: 3.532A pdb=" N SER e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 66 Processing helix chain 'e' and resid 70 through 82 Processing helix chain 'e' and resid 87 through 98 Processing helix chain 'e' and resid 99 through 108 Processing helix chain 'e' and resid 114 through 122 removed outlier: 3.576A pdb=" N VAL e 120 " --> pdb=" O ALA e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 152 removed outlier: 3.774A pdb=" N LYS e 152 " --> pdb=" O GLU e 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 149 through 152' Processing helix chain 'e' and resid 154 through 165 removed outlier: 3.801A pdb=" N LYS e 158 " --> pdb=" O GLN e 154 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU e 162 " --> pdb=" O LYS e 158 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU e 163 " --> pdb=" O ASN e 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA e 165 " --> pdb=" O ILE e 161 " (cutoff:3.500A) Processing helix chain 'e' and resid 198 through 206 removed outlier: 4.064A pdb=" N ILE e 202 " --> pdb=" O ASN e 198 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 67 Processing helix chain 'f' and resid 108 through 117 removed outlier: 3.545A pdb=" N ALA f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL f 113 " --> pdb=" O ALA f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 131 through 146 Processing helix chain 'f' and resid 148 through 157 Processing helix chain 'g' and resid 13 through 17 removed outlier: 4.080A pdb=" N ASP g 16 " --> pdb=" O ASP g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 31 removed outlier: 3.563A pdb=" N GLU g 23 " --> pdb=" O VAL g 19 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 80 Processing helix chain 'i' and resid 6 through 20 Processing helix chain 'i' and resid 30 through 43 removed outlier: 3.617A pdb=" N VAL i 39 " --> pdb=" O ALA i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 120 Processing helix chain 'l' and resid 58 through 74 Processing helix chain 'l' and resid 75 through 77 No H-bonds generated for 'chain 'l' and resid 75 through 77' Processing helix chain 'l' and resid 92 through 100 removed outlier: 4.122A pdb=" N VAL l 96 " --> pdb=" O ARG l 92 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 10 Processing helix chain 'm' and resid 21 through 25 removed outlier: 3.543A pdb=" N LYS m 25 " --> pdb=" O PRO m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 118 removed outlier: 3.640A pdb=" N GLY m 118 " --> pdb=" O SER m 115 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 39 Processing helix chain 'p' and resid 39 through 46 removed outlier: 3.681A pdb=" N ALA p 45 " --> pdb=" O GLY p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 74 removed outlier: 3.553A pdb=" N ARG p 54 " --> pdb=" O HIS p 50 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY p 55 " --> pdb=" O HIS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 86 removed outlier: 3.590A pdb=" N TYR p 78 " --> pdb=" O ASP p 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 63 Processing helix chain 'q' and resid 68 through 78 Processing helix chain 's' and resid 25 through 30 Processing helix chain 's' and resid 31 through 33 No H-bonds generated for 'chain 's' and resid 31 through 33' Processing helix chain 's' and resid 41 through 46 Processing helix chain 's' and resid 48 through 65 Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 43 through 64 Proline residue: u 56 - end of helix Processing helix chain 'u' and resid 68 through 85 removed outlier: 3.541A pdb=" N ALA u 85 " --> pdb=" O ALA u 81 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 26 removed outlier: 3.527A pdb=" N ARG v 17 " --> pdb=" O ASP v 13 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU v 24 " --> pdb=" O LYS v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 34 Processing helix chain 'v' and resid 40 through 60 Processing sheet with id=AA1, first strand: chain 'c' and resid 18 through 21 removed outlier: 5.349A pdb=" N PHE c 18 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE c 43 " --> pdb=" O PHE c 18 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS c 20 " --> pdb=" O HIS c 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY c 35 " --> pdb=" O ILE c 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 93 through 94 removed outlier: 8.034A pdb=" N VAL c 94 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE c 71 " --> pdb=" O VAL c 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 125 through 127 Processing sheet with id=AA4, first strand: chain 'f' and resid 11 through 23 removed outlier: 6.566A pdb=" N LEU f 35 " --> pdb=" O VAL f 15 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL f 17 " --> pdb=" O THR f 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR f 33 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG f 19 " --> pdb=" O SER f 31 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER f 31 " --> pdb=" O ARG f 19 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA f 21 " --> pdb=" O ILE f 29 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE f 29 " --> pdb=" O ALA f 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 84 through 88 removed outlier: 6.383A pdb=" N ILE f 105 " --> pdb=" O ALA f 124 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N CYS f 126 " --> pdb=" O ILE f 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'g' and resid 35 through 46 removed outlier: 6.435A pdb=" N ASN g 63 " --> pdb=" O HIS g 37 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU g 39 " --> pdb=" O LEU g 61 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU g 61 " --> pdb=" O LEU g 39 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP g 41 " --> pdb=" O TYR g 59 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR g 59 " --> pdb=" O ASP g 41 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY g 43 " --> pdb=" O ALA g 57 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA g 57 " --> pdb=" O GLY g 43 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N HIS g 3 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG g 91 " --> pdb=" O HIS g 3 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU g 5 " --> pdb=" O ILE g 89 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE g 89 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL g 7 " --> pdb=" O ASN g 87 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN g 87 " --> pdb=" O VAL g 7 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU g 9 " --> pdb=" O ILE g 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 24 through 28 removed outlier: 6.168A pdb=" N THR i 59 " --> pdb=" O VAL i 51 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL i 51 " --> pdb=" O THR i 59 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR i 61 " --> pdb=" O VAL i 49 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL i 49 " --> pdb=" O THR i 61 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR i 63 " --> pdb=" O SER i 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'i' and resid 66 through 67 removed outlier: 3.739A pdb=" N LYS i 70 " --> pdb=" O PHE i 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 75 through 78 removed outlier: 5.583A pdb=" N VAL i 126 " --> pdb=" O SER i 106 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER i 106 " --> pdb=" O VAL i 126 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA i 128 " --> pdb=" O ILE i 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 40 through 45 removed outlier: 6.821A pdb=" N ILE l 33 " --> pdb=" O LEU l 41 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP l 43 " --> pdb=" O VAL l 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL l 31 " --> pdb=" O TRP l 43 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU l 81 " --> pdb=" O ILE l 106 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER l 108 " --> pdb=" O LEU l 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 29 through 40 removed outlier: 6.649A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N TYR m 95 " --> pdb=" O GLU m 62 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER m 64 " --> pdb=" O TYR m 95 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR m 97 " --> pdb=" O SER m 64 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR m 66 " --> pdb=" O THR m 97 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER m 78 " --> pdb=" O CYS m 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'q' and resid 50 through 51 removed outlier: 4.892A pdb=" N ILE q 19 " --> pdb=" O ILE q 36 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE q 38 " --> pdb=" O TYR q 17 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR q 17 " --> pdb=" O PHE q 38 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL q 2 " --> pdb=" O GLN q 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'r' and resid 8 through 15 removed outlier: 16.782A pdb=" N THR r 8 " --> pdb=" O ARG r 29 " (cutoff:3.500A) removed outlier: 12.917A pdb=" N ARG r 29 " --> pdb=" O THR r 8 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR r 10 " --> pdb=" O GLU r 27 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU r 27 " --> pdb=" O THR r 10 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL r 23 " --> pdb=" O VAL r 14 " (cutoff:3.500A) removed outlier: 15.857A pdb=" N LYS r 72 " --> pdb=" O SER r 42 " (cutoff:3.500A) removed outlier: 13.654A pdb=" N LYS r 44 " --> pdb=" O LYS r 72 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N TRP r 74 " --> pdb=" O LYS r 44 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HIS r 46 " --> pdb=" O TRP r 74 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU r 76 " --> pdb=" O HIS r 46 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS r 48 " --> pdb=" O LEU r 76 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU r 78 " --> pdb=" O HIS r 48 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS r 72 " --> pdb=" O ILE r 68 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP r 74 " --> pdb=" O ARG r 66 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ARG r 66 " --> pdb=" O TRP r 74 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N LEU r 76 " --> pdb=" O GLU r 64 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLU r 64 " --> pdb=" O LEU r 76 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU r 78 " --> pdb=" O ILE r 62 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE r 62 " --> pdb=" O GLU r 78 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL r 80 " --> pdb=" O VAL r 60 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL r 60 " --> pdb=" O VAL r 80 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 912 hydrogen bonds 1386 hydrogen bond angles 0 basepair planarities 368 basepair parallelities 597 stacking parallelities Total time for adding SS restraints: 30.14 Time building geometry restraints manager: 17.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4078 1.32 - 1.44: 15122 1.44 - 1.56: 14711 1.56 - 1.69: 2075 1.69 - 1.81: 48 Bond restraints: 36034 Sorted by residual: bond pdb=" C ASP e 192 " pdb=" N LEU e 193 " ideal model delta sigma weight residual 1.333 1.280 0.052 2.74e-02 1.33e+03 3.63e+00 bond pdb=" CA GLY f 107 " pdb=" C GLY f 107 " ideal model delta sigma weight residual 1.520 1.506 0.014 7.30e-03 1.88e+04 3.55e+00 bond pdb=" C3' C 2 99 " pdb=" C2' C 2 99 " ideal model delta sigma weight residual 1.525 1.498 0.027 1.50e-02 4.44e+03 3.29e+00 bond pdb=" N3 C 2 172 " pdb=" C4 C 2 172 " ideal model delta sigma weight residual 1.334 1.301 0.033 2.00e-02 2.50e+03 2.80e+00 bond pdb=" C8 G 2 100 " pdb=" N7 G 2 100 " ideal model delta sigma weight residual 1.305 1.272 0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 36029 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.91: 5784 105.91 - 112.95: 20856 112.95 - 120.00: 12766 120.00 - 127.04: 11899 127.04 - 134.08: 2587 Bond angle restraints: 53892 Sorted by residual: angle pdb=" C2' G 2 100 " pdb=" C1' G 2 100 " pdb=" N9 G 2 100 " ideal model delta sigma weight residual 112.00 103.64 8.36 1.50e+00 4.44e-01 3.11e+01 angle pdb=" C2' C 2 99 " pdb=" C1' C 2 99 " pdb=" N1 C 2 99 " ideal model delta sigma weight residual 114.00 107.05 6.95 1.50e+00 4.44e-01 2.15e+01 angle pdb=" C GLU f 54 " pdb=" N VAL f 55 " pdb=" CA VAL f 55 " ideal model delta sigma weight residual 120.33 123.93 -3.60 8.00e-01 1.56e+00 2.03e+01 angle pdb=" C ALA f 106 " pdb=" N GLY f 107 " pdb=" CA GLY f 107 " ideal model delta sigma weight residual 122.73 118.85 3.88 9.30e-01 1.16e+00 1.74e+01 angle pdb=" O4' G 2 612 " pdb=" C1' G 2 612 " pdb=" N9 G 2 612 " ideal model delta sigma weight residual 108.20 114.03 -5.83 1.50e+00 4.44e-01 1.51e+01 ... (remaining 53887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 18328 35.68 - 71.36: 820 71.36 - 107.05: 63 107.05 - 142.73: 4 142.73 - 178.41: 7 Dihedral angle restraints: 19222 sinusoidal: 14936 harmonic: 4286 Sorted by residual: dihedral pdb=" O4' C 2 172 " pdb=" C1' C 2 172 " pdb=" N1 C 2 172 " pdb=" C2 C 2 172 " ideal model delta sinusoidal sigma weight residual -160.00 18.41 -178.41 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 435 " pdb=" C1' U 2 435 " pdb=" N1 U 2 435 " pdb=" C2 U 2 435 " ideal model delta sinusoidal sigma weight residual -160.00 -10.94 -149.06 1 1.50e+01 4.44e-03 7.93e+01 dihedral pdb=" O4' U 2 419 " pdb=" C1' U 2 419 " pdb=" N1 U 2 419 " pdb=" C2 U 2 419 " ideal model delta sinusoidal sigma weight residual 200.00 55.66 144.34 1 1.50e+01 4.44e-03 7.73e+01 ... (remaining 19219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 6252 0.080 - 0.161: 621 0.161 - 0.241: 42 0.241 - 0.321: 3 0.321 - 0.401: 1 Chirality restraints: 6919 Sorted by residual: chirality pdb=" C2' G 2 100 " pdb=" C3' G 2 100 " pdb=" O2' G 2 100 " pdb=" C1' G 2 100 " both_signs ideal model delta sigma weight residual False -2.75 -2.35 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1' A 2 5 " pdb=" O4' A 2 5 " pdb=" C2' A 2 5 " pdb=" N9 A 2 5 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1' A 2 294 " pdb=" O4' A 2 294 " pdb=" C2' A 2 294 " pdb=" N9 A 2 294 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 6916 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 99 " 0.090 2.00e-02 2.50e+03 4.64e-02 4.84e+01 pdb=" N1 C 2 99 " -0.099 2.00e-02 2.50e+03 pdb=" C2 C 2 99 " -0.018 2.00e-02 2.50e+03 pdb=" O2 C 2 99 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C 2 99 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C 2 99 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C 2 99 " 0.027 2.00e-02 2.50e+03 pdb=" C5 C 2 99 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C 2 99 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 100 " 0.087 2.00e-02 2.50e+03 3.87e-02 4.49e+01 pdb=" N9 G 2 100 " -0.097 2.00e-02 2.50e+03 pdb=" C8 G 2 100 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 2 100 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 100 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 2 100 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G 2 100 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G 2 100 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G 2 100 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 2 100 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 2 100 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G 2 100 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 612 " 0.082 2.00e-02 2.50e+03 3.48e-02 3.62e+01 pdb=" N9 G 2 612 " -0.080 2.00e-02 2.50e+03 pdb=" C8 G 2 612 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G 2 612 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G 2 612 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G 2 612 " 0.014 2.00e-02 2.50e+03 pdb=" O6 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" C2 G 2 612 " -0.008 2.00e-02 2.50e+03 pdb=" N2 G 2 612 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G 2 612 " -0.013 2.00e-02 2.50e+03 pdb=" C4 G 2 612 " -0.017 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 147 2.44 - 3.05: 19077 3.05 - 3.67: 62268 3.67 - 4.28: 98634 4.28 - 4.90: 129249 Nonbonded interactions: 309375 Sorted by model distance: nonbonded pdb=" OP1 G 41502 " pdb="MG MG 41602 " model vdw 1.825 2.170 nonbonded pdb=" OP1 C 2 573 " pdb="MG MG 21651 " model vdw 1.936 2.170 nonbonded pdb=" OP1 A 41497 " pdb="MG MG 41602 " model vdw 1.944 2.170 nonbonded pdb=" OP2 G 2 285 " pdb="MG MG 21602 " model vdw 1.948 2.170 nonbonded pdb=" OP2 U 2 557 " pdb="MG MG 21613 " model vdw 1.979 2.170 ... (remaining 309370 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 1040 5.49 5 Mg 56 5.21 5 S 28 5.16 5 C 16706 2.51 5 N 6236 2.21 5 O 9213 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.770 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.310 Process input model: 114.410 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.010 0.079 36034 Z= 0.587 Angle : 0.807 8.363 53892 Z= 0.421 Chirality : 0.049 0.401 6919 Planarity : 0.006 0.046 2984 Dihedral : 16.247 178.410 16456 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 8.22 % 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: -3.30 (0.18), residues: 1470 helix: -1.73 (0.18), residues: 594 sheet: -1.59 (0.29), residues: 249 loop : -2.83 (0.20), residues: 627 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 251 time to evaluate : 2.021 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 51 residues processed: 313 average time/residue: 1.5176 time to fit residues: 562.4571 Evaluate side-chains 297 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 246 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 39 residues processed: 12 average time/residue: 0.3825 time to fit residues: 9.8102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 224 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN e 128 ASN e 148 HIS e 177 HIS g 17 GLN g 52 ASN g 63 ASN i 18 GLN i 42 GLN l 21 HIS l 37 GLN l 49 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 46 HIS p 62 GLN q 44 GLN q 46 GLN u 6 GLN v 57 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 36034 Z= 0.162 Angle : 0.528 6.922 53892 Z= 0.279 Chirality : 0.035 0.192 6919 Planarity : 0.004 0.036 2984 Dihedral : 14.471 178.589 14098 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 7.52 % 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: -1.64 (0.21), residues: 1470 helix: 0.07 (0.21), residues: 609 sheet: -1.16 (0.31), residues: 254 loop : -2.24 (0.22), residues: 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 266 time to evaluate : 2.075 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 44 residues processed: 323 average time/residue: 1.4276 time to fit residues: 549.6518 Evaluate side-chains 293 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 249 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 9 average time/residue: 0.3003 time to fit residues: 7.1699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 28 GLN g 52 ASN i 42 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 37 ASN p 62 GLN q 46 GLN v 57 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 36034 Z= 0.425 Angle : 0.673 7.095 53892 Z= 0.346 Chirality : 0.042 0.225 6919 Planarity : 0.005 0.040 2984 Dihedral : 14.588 178.567 14098 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 8.12 % 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: -1.29 (0.21), residues: 1470 helix: 0.39 (0.21), residues: 608 sheet: -0.91 (0.31), residues: 259 loop : -2.12 (0.22), residues: 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 251 time to evaluate : 2.204 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 56 residues processed: 307 average time/residue: 1.4632 time to fit residues: 535.8996 Evaluate side-chains 306 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 250 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 43 residues processed: 14 average time/residue: 0.3911 time to fit residues: 11.2586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 42 HIS e 177 HIS g 28 GLN g 52 ASN i 41 GLN i 42 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 37 ASN p 62 GLN p 75 HIS q 46 GLN v 57 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 36034 Z= 0.166 Angle : 0.519 7.149 53892 Z= 0.274 Chirality : 0.034 0.193 6919 Planarity : 0.004 0.035 2984 Dihedral : 14.350 178.946 14098 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 6.81 % 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: -0.63 (0.22), residues: 1470 helix: 1.05 (0.22), residues: 604 sheet: -0.66 (0.33), residues: 258 loop : -1.84 (0.22), residues: 608 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 268 time to evaluate : 2.041 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 43 residues processed: 319 average time/residue: 1.4357 time to fit residues: 548.8759 Evaluate side-chains 296 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 36 residues processed: 8 average time/residue: 0.3419 time to fit residues: 7.4126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 203 optimal weight: 0.0470 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 214 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 36034 Z= 0.209 Angle : 0.535 7.330 53892 Z= 0.281 Chirality : 0.035 0.200 6919 Planarity : 0.004 0.034 2984 Dihedral : 14.289 178.989 14098 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 6.51 % 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: -0.37 (0.22), residues: 1470 helix: 1.26 (0.22), residues: 604 sheet: -0.46 (0.34), residues: 257 loop : -1.71 (0.23), residues: 609 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 259 time to evaluate : 2.068 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 45 residues processed: 303 average time/residue: 1.4409 time to fit residues: 522.1692 Evaluate side-chains 297 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 252 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 37 residues processed: 8 average time/residue: 0.2995 time to fit residues: 6.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 0.4980 chunk 198 optimal weight: 0.0010 chunk 110 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 42 HIS e 56 GLN e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 35 GLN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 36034 Z= 0.182 Angle : 0.527 7.683 53892 Z= 0.277 Chirality : 0.034 0.197 6919 Planarity : 0.004 0.032 2984 Dihedral : 14.288 179.066 14098 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 5.61 % 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: -0.26 (0.22), residues: 1470 helix: 1.37 (0.22), residues: 604 sheet: -0.45 (0.34), residues: 258 loop : -1.66 (0.23), residues: 608 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 1.984 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 45 residues processed: 294 average time/residue: 1.4352 time to fit residues: 505.7661 Evaluate side-chains 291 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 246 time to evaluate : 1.976 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 37 residues processed: 8 average time/residue: 0.8357 time to fit residues: 10.8505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 42 HIS e 56 GLN e 177 HIS g 52 ASN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN ** p 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 35 GLN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 36034 Z= 0.167 Angle : 0.520 7.263 53892 Z= 0.274 Chirality : 0.034 0.195 6919 Planarity : 0.004 0.032 2984 Dihedral : 14.284 179.128 14098 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 5.51 % 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: -0.21 (0.22), residues: 1470 helix: 1.42 (0.22), residues: 604 sheet: -0.43 (0.34), residues: 258 loop : -1.63 (0.23), residues: 608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 252 time to evaluate : 1.997 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 46 residues processed: 294 average time/residue: 1.4071 time to fit residues: 496.1846 Evaluate side-chains 294 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 248 time to evaluate : 1.950 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 37 residues processed: 9 average time/residue: 0.5628 time to fit residues: 9.5649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 216 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 52 ASN i 41 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 35 GLN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 36034 Z= 0.363 Angle : 0.627 7.285 53892 Z= 0.324 Chirality : 0.040 0.218 6919 Planarity : 0.005 0.038 2984 Dihedral : 14.450 179.130 14098 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 5.81 % 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: -0.42 (0.22), residues: 1470 helix: 1.14 (0.21), residues: 610 sheet: -0.40 (0.34), residues: 254 loop : -1.73 (0.23), residues: 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 2.053 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 47 residues processed: 297 average time/residue: 1.4043 time to fit residues: 499.8405 Evaluate side-chains 299 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 36 residues processed: 11 average time/residue: 0.5119 time to fit residues: 10.8498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 56 GLN e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN ** p 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 62 GLN q 46 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 36034 Z= 0.174 Angle : 0.535 8.643 53892 Z= 0.280 Chirality : 0.034 0.199 6919 Planarity : 0.004 0.033 2984 Dihedral : 14.358 179.385 14098 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 4.71 % 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: -0.15 (0.22), residues: 1470 helix: 1.43 (0.22), residues: 605 sheet: -0.40 (0.34), residues: 257 loop : -1.56 (0.23), residues: 608 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 248 time to evaluate : 1.995 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 39 residues processed: 287 average time/residue: 1.4308 time to fit residues: 492.2151 Evaluate side-chains 281 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 35 residues processed: 4 average time/residue: 0.5938 time to fit residues: 5.5682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 chunk 163 optimal weight: 4.9990 chunk 246 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 chunk 195 optimal weight: 0.0570 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 0.0570 chunk 155 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 56 GLN e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 35 GLN p 48 HIS p 62 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 36034 Z= 0.148 Angle : 0.510 8.683 53892 Z= 0.268 Chirality : 0.033 0.189 6919 Planarity : 0.004 0.032 2984 Dihedral : 14.253 179.489 14098 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 4.21 % 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: 0.05 (0.22), residues: 1470 helix: 1.61 (0.22), residues: 605 sheet: -0.40 (0.34), residues: 258 loop : -1.42 (0.24), residues: 607 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 250 time to evaluate : 2.003 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 35 residues processed: 288 average time/residue: 1.4095 time to fit residues: 487.7409 Evaluate side-chains 279 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 244 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 35 residues processed: 0 time to fit residues: 2.1247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 201 optimal weight: 0.0000 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 56 GLN e 91 ASN e 177 HIS g 52 ASN i 41 GLN l 107 ASN m 111 ASN p 20 ASN p 35 GLN p 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105891 restraints weight = 39224.204| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 0.33 r_work: 0.3189 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 1.00 restraints_weight: 0.2500 r_work: 0.3105 rms_B_bonded: 1.65 restraints_weight: 0.1250 r_work: 0.2993 rms_B_bonded: 3.32 restraints_weight: 0.0625 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 36034 Z= 0.336 Angle : 0.610 8.864 53892 Z= 0.316 Chirality : 0.039 0.212 6919 Planarity : 0.005 0.036 2984 Dihedral : 14.360 179.369 14098 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 4.51 % 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: -0.19 (0.22), residues: 1470 helix: 1.32 (0.21), residues: 612 sheet: -0.34 (0.34), residues: 254 loop : -1.55 (0.23), residues: 604 =============================================================================== Job complete usr+sys time: 7968.43 seconds wall clock time: 144 minutes 50.94 seconds (8690.94 seconds total)