Starting phenix.real_space_refine (version: dev) on Mon May 16 16:35:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/05_2022/6ypu_10869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/05_2022/6ypu_10869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/05_2022/6ypu_10869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/05_2022/6ypu_10869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/05_2022/6ypu_10869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/05_2022/6ypu_10869_updated.pdb" } resolution = 2.9 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= 0.003 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 "e TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 33322 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': 324, 'rna2p_pur': 72, 'rna3p_pur': 457, 'rna2p_pyr': 41} Link IDs: {'rna3p': 780, 'rna2p': 113} 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Unusual residues: {' MG': 53} Classifications: {'undetermined': 53} Link IDs: {None: 52} Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 46 Unusual residues: {' MG': 6, 'AKN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 18.90, per 1000 atoms: 0.57 Number of scatterers: 33322 At special positions: 0 Unit cell: (206.51, 159.43, 153.01, 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 59 11.99 O 9226 8.00 N 6241 7.00 C 16728 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: 15.36 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 51 helices and 13 sheets defined 35.4% alpha, 15.4% beta 331 base pairs and 588 stacking pairs defined. Time for finding SS restraints: 16.47 Creating SS restraints... Processing helix chain 'c' and resid 27 through 29 No H-bonds generated for 'chain 'c' and resid 27 through 29' Processing helix chain 'c' and resid 45 through 63 Proline residue: c 50 - end of helix removed outlier: 3.752A pdb=" N ASN c 53 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP c 54 " --> pdb=" O PRO c 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE c 58 " --> pdb=" O ASP c 54 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA c 59 " --> pdb=" O ALA c 55 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN c 60 " --> pdb=" O LEU c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 87 removed outlier: 4.392A pdb=" N GLU c 84 " --> pdb=" O ASN c 80 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA c 86 " --> pdb=" O ILE c 82 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN c 87 " --> pdb=" O ARG c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 121 removed outlier: 4.704A pdb=" N GLN c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER c 112 " --> pdb=" O THR c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 133 through 148 Processing helix chain 'c' and resid 151 through 153 No H-bonds generated for 'chain 'c' and resid 151 through 153' Processing helix chain 'c' and resid 172 through 181 removed outlier: 3.688A pdb=" N GLU c 177 " --> pdb=" O ILE c 173 " (cutoff:3.500A) Processing helix chain 'c' and resid 209 through 224 Processing helix chain 'e' and resid 10 through 15 removed outlier: 3.615A pdb=" N ARG e 14 " --> pdb=" O LYS e 10 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU e 15 " --> pdb=" O LEU e 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 10 through 15' Processing helix chain 'e' and resid 54 through 67 Processing helix chain 'e' and resid 71 through 81 Processing helix chain 'e' and resid 88 through 97 removed outlier: 3.634A pdb=" N LEU e 92 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU e 93 " --> pdb=" O GLY e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 100 through 106 Processing helix chain 'e' and resid 113 through 121 removed outlier: 4.267A pdb=" N GLN e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 129 No H-bonds generated for 'chain 'e' and resid 127 through 129' Processing helix chain 'e' and resid 149 through 151 No H-bonds generated for 'chain 'e' and resid 149 through 151' Processing helix chain 'e' and resid 156 through 164 removed outlier: 3.952A pdb=" N ALA e 160 " --> pdb=" O ARG e 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU e 162 " --> pdb=" O LYS e 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 207 removed outlier: 3.904A pdb=" N GLU e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER e 207 " --> pdb=" O VAL e 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 67 Processing helix chain 'f' and resid 108 through 115 removed outlier: 3.745A pdb=" N ALA f 112 " --> pdb=" O ALA f 109 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU f 115 " --> pdb=" O ALA f 112 " (cutoff:3.500A) Processing helix chain 'f' and resid 132 through 144 Processing helix chain 'f' and resid 149 through 155 removed outlier: 4.022A pdb=" N ALA f 153 " --> pdb=" O PRO f 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 14 No H-bonds generated for 'chain 'g' and resid 12 through 14' Processing helix chain 'g' and resid 19 through 31 removed outlier: 4.155A pdb=" N ARG g 24 " --> pdb=" O GLY g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 79 Processing helix chain 'i' and resid 7 through 20 Processing helix chain 'i' and resid 31 through 42 Processing helix chain 'i' and resid 96 through 99 Processing helix chain 'i' and resid 114 through 120 removed outlier: 3.646A pdb=" N ALA i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA i 120 " --> pdb=" O ALA i 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 56 Processing helix chain 'l' and resid 59 through 76 removed outlier: 4.145A pdb=" N ASP l 75 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 90 through 100 removed outlier: 4.125A pdb=" N GLU l 93 " --> pdb=" O PRO l 90 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER l 94 " --> pdb=" O GLY l 91 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA l 95 " --> pdb=" O ARG l 92 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 9 Processing helix chain 'm' and resid 114 through 116 No H-bonds generated for 'chain 'm' and resid 114 through 116' Processing helix chain 'p' and resid 5 through 15 removed outlier: 3.505A pdb=" N ILE p 12 " --> pdb=" O ARG p 8 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS p 14 " --> pdb=" O GLU p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 25 through 45 removed outlier: 3.795A pdb=" N GLN p 40 " --> pdb=" O ILE p 36 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY p 41 " --> pdb=" O ASN p 37 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS p 42 " --> pdb=" O ASP p 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA p 45 " --> pdb=" O GLY p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 73 removed outlier: 3.712A pdb=" N LYS p 65 " --> pdb=" O ASN p 61 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY p 72 " --> pdb=" O ASP p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 85 Processing helix chain 'q' and resid 54 through 63 Processing helix chain 'q' and resid 71 through 77 removed outlier: 3.557A pdb=" N ALA q 76 " --> pdb=" O ALA q 72 " (cutoff:3.500A) Processing helix chain 's' and resid 26 through 28 No H-bonds generated for 'chain 's' and resid 26 through 28' Processing helix chain 's' and resid 30 through 32 No H-bonds generated for 'chain 's' and resid 30 through 32' Processing helix chain 's' and resid 42 through 45 No H-bonds generated for 'chain 's' and resid 42 through 45' Processing helix chain 's' and resid 49 through 65 removed outlier: 3.583A pdb=" N ARG s 53 " --> pdb=" O ALA s 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN s 54 " --> pdb=" O ARG s 50 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR s 64 " --> pdb=" O LYS s 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 41 removed outlier: 3.634A pdb=" N LYS u 16 " --> pdb=" O ARG u 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER u 23 " --> pdb=" O LYS u 19 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU u 24 " --> pdb=" O HIS u 20 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY u 41 " --> pdb=" O SER u 37 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 51 Processing helix chain 'u' and resid 55 through 63 Processing helix chain 'u' and resid 69 through 80 Processing helix chain 'v' and resid 12 through 25 removed outlier: 3.982A pdb=" N ILE v 16 " --> pdb=" O VAL v 12 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG v 17 " --> pdb=" O ASP v 13 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG v 18 " --> pdb=" O VAL v 14 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG v 21 " --> pdb=" O ARG v 17 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU v 24 " --> pdb=" O LYS v 20 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS v 25 " --> pdb=" O ARG v 21 " (cutoff:3.500A) Processing helix chain 'v' and resid 30 through 33 No H-bonds generated for 'chain 'v' and resid 30 through 33' Processing helix chain 'v' and resid 41 through 57 removed outlier: 3.526A pdb=" N ALA v 50 " --> pdb=" O LYS v 46 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN v 57 " --> pdb=" O VAL v 53 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'c' and resid 70 through 72 removed outlier: 8.004A pdb=" N VAL c 165 " --> pdb=" O PRO c 184 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE c 186 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR c 200 " --> pdb=" O GLY c 187 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL c 189 " --> pdb=" O TYR c 200 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE c 202 " --> pdb=" O VAL c 189 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'f' and resid 45 through 52 removed outlier: 6.632A pdb=" N VAL f 37 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU f 14 " --> pdb=" O VAL f 37 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY f 39 " --> pdb=" O GLU f 12 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU f 12 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'f' and resid 84 through 88 Processing sheet with id= D, first strand: chain 'g' and resid 44 through 46 removed outlier: 3.734A pdb=" N ILE g 6 " --> pdb=" O MET g 62 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS g 3 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG g 86 " --> pdb=" O LEU g 9 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS g 11 " --> pdb=" O ILE g 84 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE g 84 " --> pdb=" O HIS g 11 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'g' and resid 35 through 39 removed outlier: 6.694A pdb=" N ASN g 63 " --> pdb=" O HIS g 37 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.772A pdb=" N ASN i 48 " --> pdb=" O THR i 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'i' and resid 76 through 78 removed outlier: 6.787A pdb=" N ILE i 104 " --> pdb=" O ILE i 127 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE i 129 " --> pdb=" O ILE i 102 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE i 102 " --> pdb=" O PHE i 129 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'l' and resid 40 through 45 removed outlier: 6.966A pdb=" N ILE l 33 " --> pdb=" O LEU l 41 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP l 43 " --> pdb=" O VAL l 31 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL l 31 " --> pdb=" O TRP l 43 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR l 45 " --> pdb=" O THR l 29 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR l 29 " --> pdb=" O THR l 45 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN l 80 " --> pdb=" O GLY l 18 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA l 20 " --> pdb=" O ASN l 80 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP l 82 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE l 22 " --> pdb=" O ASP l 82 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU l 84 " --> pdb=" O ILE l 22 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA l 24 " --> pdb=" O LEU l 84 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS l 86 " --> pdb=" O ALA l 24 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'm' and resid 95 through 97 removed outlier: 6.379A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'q' and resid 2 through 8 Processing sheet with id= K, first strand: chain 'q' and resid 37 through 39 Processing sheet with id= L, first strand: chain 'r' and resid 74 through 76 removed outlier: 16.880A pdb=" N THR r 8 " --> pdb=" O ARG r 29 " (cutoff:3.500A) removed outlier: 13.372A pdb=" N ARG r 29 " --> pdb=" O THR r 8 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR r 10 " --> pdb=" O GLU r 27 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU r 27 " --> pdb=" O THR r 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL r 23 " --> pdb=" O VAL r 14 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'r' and resid 59 through 61 removed outlier: 3.940A pdb=" N VAL r 59 " --> pdb=" O GLU r 81 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU r 81 " --> pdb=" O VAL r 59 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR r 61 " --> pdb=" O VAL r 79 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL r 79 " --> pdb=" O THR r 61 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 397 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 832 hydrogen bonds 1280 hydrogen bond angles 0 basepair planarities 331 basepair parallelities 588 stacking parallelities Total time for adding SS restraints: 30.69 Time building geometry restraints manager: 16.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3407 1.30 - 1.43: 15692 1.43 - 1.56: 14854 1.56 - 1.68: 2075 1.68 - 1.81: 48 Bond restraints: 36076 Sorted by residual: bond pdb=" C35 AKN 41607 " pdb=" N12 AKN 41607 " ideal model delta sigma weight residual 1.339 1.471 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C24 AKN 41607 " pdb=" C26 AKN 41607 " ideal model delta sigma weight residual 1.532 1.450 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C7 AKN 41607 " pdb=" O8 AKN 41607 " ideal model delta sigma weight residual 1.420 1.496 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C28 AKN 41607 " pdb=" O29 AKN 41607 " ideal model delta sigma weight residual 1.421 1.491 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 AKN 41607 " pdb=" C5 AKN 41607 " ideal model delta sigma weight residual 1.525 1.457 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 36071 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.19: 5114 105.19 - 112.47: 20281 112.47 - 119.75: 13205 119.75 - 127.03: 12696 127.03 - 134.32: 2657 Bond angle restraints: 53953 Sorted by residual: angle pdb=" N TYR e 53 " pdb=" CA TYR e 53 " pdb=" C TYR e 53 " ideal model delta sigma weight residual 114.56 106.68 7.88 1.27e+00 6.20e-01 3.85e+01 angle pdb=" N VAL r 14 " pdb=" CA VAL r 14 " pdb=" C VAL r 14 " ideal model delta sigma weight residual 113.71 109.26 4.45 9.50e-01 1.11e+00 2.20e+01 angle pdb=" O4' G 2 612 " pdb=" C1' G 2 612 " pdb=" N9 G 2 612 " ideal model delta sigma weight residual 108.20 114.93 -6.73 1.50e+00 4.44e-01 2.01e+01 angle pdb=" C2' A 2 360 " pdb=" C1' A 2 360 " pdb=" N9 A 2 360 " ideal model delta sigma weight residual 112.00 118.14 -6.14 1.50e+00 4.44e-01 1.67e+01 angle pdb=" O3' G 2 186 " pdb=" C3' G 2 186 " pdb=" C2' G 2 186 " ideal model delta sigma weight residual 113.70 119.35 -5.65 1.50e+00 4.44e-01 1.42e+01 ... (remaining 53948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 18365 35.76 - 71.53: 786 71.53 - 107.29: 54 107.29 - 143.05: 7 143.05 - 178.82: 11 Dihedral angle restraints: 19223 sinusoidal: 14937 harmonic: 4286 Sorted by residual: dihedral pdb=" O4' C 2 131 " pdb=" C1' C 2 131 " pdb=" N1 C 2 131 " pdb=" C2 C 2 131 " ideal model delta sinusoidal sigma weight residual -160.00 18.82 -178.82 1 1.50e+01 4.44e-03 8.53e+01 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 200.00 24.73 175.27 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 2 463 " pdb=" C1' U 2 463 " pdb=" N1 U 2 463 " pdb=" C2 U 2 463 " ideal model delta sinusoidal sigma weight residual -160.00 14.91 -174.91 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 19220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5698 0.072 - 0.145: 1095 0.145 - 0.217: 123 0.217 - 0.290: 15 0.290 - 0.362: 4 Chirality restraints: 6935 Sorted by residual: chirality pdb=" C1' U 2 361 " pdb=" O4' U 2 361 " pdb=" C2' U 2 361 " pdb=" N1 U 2 361 " both_signs ideal model delta sigma weight residual False 2.47 2.10 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C3' G 2 186 " pdb=" C4' G 2 186 " pdb=" O3' G 2 186 " pdb=" C2' G 2 186 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1' G 41527 " pdb=" O4' G 41527 " pdb=" C2' G 41527 " pdb=" N9 G 41527 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 6932 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 612 " 0.066 2.00e-02 2.50e+03 2.81e-02 2.38e+01 pdb=" N9 G 2 612 " -0.066 2.00e-02 2.50e+03 pdb=" C8 G 2 612 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G 2 612 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 2 612 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 612 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G 2 612 " 0.008 2.00e-02 2.50e+03 pdb=" C2 G 2 612 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G 2 612 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 2 612 " -0.015 2.00e-02 2.50e+03 pdb=" C4 G 2 612 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 360 " -0.060 2.00e-02 2.50e+03 2.82e-02 2.19e+01 pdb=" N9 A 2 360 " 0.059 2.00e-02 2.50e+03 pdb=" C8 A 2 360 " 0.013 2.00e-02 2.50e+03 pdb=" N7 A 2 360 " -0.017 2.00e-02 2.50e+03 pdb=" C5 A 2 360 " 0.019 2.00e-02 2.50e+03 pdb=" C6 A 2 360 " -0.020 2.00e-02 2.50e+03 pdb=" N6 A 2 360 " -0.015 2.00e-02 2.50e+03 pdb=" N1 A 2 360 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 360 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A 2 360 " -0.000 2.00e-02 2.50e+03 pdb=" C4 A 2 360 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 331 " 0.055 2.00e-02 2.50e+03 2.97e-02 1.99e+01 pdb=" N1 C 2 331 " -0.068 2.00e-02 2.50e+03 pdb=" C2 C 2 331 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C 2 331 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C 2 331 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C 2 331 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C 2 331 " 0.014 2.00e-02 2.50e+03 pdb=" C5 C 2 331 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C 2 331 " -0.008 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 124 2.46 - 3.07: 19319 3.07 - 3.68: 57233 3.68 - 4.29: 94385 4.29 - 4.90: 125258 Nonbonded interactions: 296319 Sorted by model distance: nonbonded pdb=" OP1 G 41502 " pdb="MG MG 41602 " model vdw 1.849 2.170 nonbonded pdb=" OP1 A 2 530 " pdb="MG MG 21636 " model vdw 1.897 2.170 nonbonded pdb=" O2 C 2 152 " pdb=" N2 G 2 161 " model vdw 1.931 2.496 nonbonded pdb=" OP2 G 2 285 " pdb="MG MG 21602 " model vdw 2.051 2.170 nonbonded pdb=" OP2 A 2 191 " pdb="MG MG 21629 " model vdw 2.056 2.170 ... (remaining 296314 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 59 5.21 5 S 28 5.16 5 C 16728 2.51 5 N 6241 2.21 5 O 9226 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: 3.990 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: 0.020 Extract box with map and model: 15.970 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.270 Process input model: 115.880 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.012 0.132 36076 Z= 0.700 Angle : 0.989 9.647 53953 Z= 0.495 Chirality : 0.057 0.362 6935 Planarity : 0.007 0.065 2985 Dihedral : 16.541 178.817 16457 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.25 % Favored : 90.54 % Rotamer Outliers : 11.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.96 (0.18), residues: 1470 helix: -2.40 (0.17), residues: 558 sheet: -1.23 (0.32), residues: 234 loop : -3.35 (0.18), residues: 678 *********************** 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 309 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 199 time to evaluate : 2.022 Fit side-chains revert: symmetry clash outliers start: 110 outliers final: 82 residues processed: 295 average time/residue: 1.3673 time to fit residues: 485.7566 Evaluate side-chains 267 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 185 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 74 residues processed: 9 average time/residue: 0.7166 time to fit residues: 10.9751 ------------------------------------------------------------------------------- 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: 0.8980 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 126 optimal weight: 0.0970 chunk 100 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 117 optimal weight: 0.0670 chunk 144 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN e 122 HIS e 154 GLN e 177 HIS f 120 HIS f 137 ASN g 58 HIS g 63 ASN i 16 ASN i 42 GLN l 49 GLN l 63 GLN m 96 HIS m 111 ASN p 42 HIS p 62 GLN q 26 ASN r 32 HIS s 52 GLN u 13 GLN u 20 HIS u 68 HIS u 70 ASN u 75 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 36076 Z= 0.116 Angle : 0.521 7.820 53953 Z= 0.275 Chirality : 0.034 0.226 6935 Planarity : 0.004 0.050 2985 Dihedral : 14.302 176.206 14099 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 9.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.21), residues: 1470 helix: -0.45 (0.22), residues: 545 sheet: -0.55 (0.33), residues: 234 loop : -2.58 (0.21), residues: 691 *********************** 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 296 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 198 time to evaluate : 2.304 Fit side-chains revert: symmetry clash outliers start: 98 outliers final: 57 residues processed: 278 average time/residue: 1.3827 time to fit residues: 462.9598 Evaluate side-chains 238 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 181 time to evaluate : 1.973 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 50 residues processed: 7 average time/residue: 0.3276 time to fit residues: 6.1649 ------------------------------------------------------------------------------- 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: 5.9990 chunk 69 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 224 optimal weight: 0.0870 chunk 242 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 overall best weight: 2.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 HIS g 28 GLN g 63 ASN i 42 GLN i 53 GLN l 27 ASN p 35 GLN p 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 36076 Z= 0.345 Angle : 0.663 8.278 53953 Z= 0.339 Chirality : 0.041 0.259 6935 Planarity : 0.005 0.055 2985 Dihedral : 14.477 179.897 14099 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.73 % Favored : 93.20 % Rotamer Outliers : 10.02 % 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: -1.91 (0.21), residues: 1470 helix: -0.22 (0.23), residues: 553 sheet: -0.43 (0.33), residues: 229 loop : -2.50 (0.21), residues: 688 *********************** 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 280 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 180 time to evaluate : 2.033 Fit side-chains revert: symmetry clash outliers start: 100 outliers final: 74 residues processed: 265 average time/residue: 1.3407 time to fit residues: 431.8015 Evaluate side-chains 252 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 178 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 66 residues processed: 9 average time/residue: 0.6795 time to fit residues: 10.6109 ------------------------------------------------------------------------------- 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: 0.0370 chunk 168 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN i 53 GLN p 61 ASN p 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 36076 Z= 0.256 Angle : 0.608 8.634 53953 Z= 0.316 Chirality : 0.039 0.251 6935 Planarity : 0.005 0.054 2985 Dihedral : 14.443 179.792 14099 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 10.02 % 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: -1.67 (0.21), residues: 1470 helix: 0.00 (0.23), residues: 553 sheet: -0.30 (0.33), residues: 234 loop : -2.40 (0.21), residues: 683 *********************** 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 275 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 175 time to evaluate : 2.024 Fit side-chains revert: symmetry clash outliers start: 100 outliers final: 77 residues processed: 259 average time/residue: 1.3372 time to fit residues: 422.2398 Evaluate side-chains 252 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 175 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 71 residues processed: 7 average time/residue: 0.3530 time to fit residues: 6.4977 ------------------------------------------------------------------------------- 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: 4.9990 chunk 135 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 203 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 0.0270 chunk 214 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 61 ASN p 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 36076 Z= 0.181 Angle : 0.570 9.858 53953 Z= 0.298 Chirality : 0.036 0.241 6935 Planarity : 0.004 0.052 2985 Dihedral : 14.382 179.446 14099 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 9.22 % 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: -1.45 (0.22), residues: 1470 helix: 0.24 (0.23), residues: 552 sheet: -0.20 (0.33), residues: 232 loop : -2.30 (0.22), residues: 686 *********************** 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 270 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 178 time to evaluate : 2.175 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 77 residues processed: 259 average time/residue: 1.3087 time to fit residues: 411.7522 Evaluate side-chains 246 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 169 time to evaluate : 2.169 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 71 residues processed: 7 average time/residue: 0.7025 time to fit residues: 9.4631 ------------------------------------------------------------------------------- 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: 5.9990 chunk 215 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 238 optimal weight: 0.0970 chunk 198 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 61 ASN p 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.074 36076 Z= 0.395 Angle : 0.705 9.158 53953 Z= 0.358 Chirality : 0.044 0.272 6935 Planarity : 0.005 0.056 2985 Dihedral : 14.601 179.861 14099 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.06 % Rotamer Outliers : 10.92 % 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: -1.59 (0.21), residues: 1470 helix: 0.06 (0.23), residues: 557 sheet: -0.31 (0.33), residues: 232 loop : -2.32 (0.22), residues: 681 *********************** 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 286 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 177 time to evaluate : 2.113 Fit side-chains revert: symmetry clash outliers start: 109 outliers final: 74 residues processed: 266 average time/residue: 1.3389 time to fit residues: 434.3056 Evaluate side-chains 250 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 176 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 66 residues processed: 8 average time/residue: 0.3412 time to fit residues: 7.1576 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 238 optimal weight: 0.0020 chunk 148 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN l 27 ASN p 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.062 36076 Z= 0.140 Angle : 0.567 8.501 53953 Z= 0.296 Chirality : 0.036 0.246 6935 Planarity : 0.004 0.053 2985 Dihedral : 14.423 178.406 14099 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 8.92 % 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: -1.21 (0.22), residues: 1470 helix: 0.44 (0.23), residues: 552 sheet: -0.10 (0.33), residues: 234 loop : -2.17 (0.22), residues: 684 *********************** 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 271 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 182 time to evaluate : 2.204 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 70 residues processed: 260 average time/residue: 1.3277 time to fit residues: 419.2170 Evaluate side-chains 242 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 172 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 67 residues processed: 4 average time/residue: 0.4013 time to fit residues: 4.8784 ------------------------------------------------------------------------------- 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: 0.1980 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 117 optimal weight: 0.0040 chunk 22 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 36076 Z= 0.246 Angle : 0.590 9.753 53953 Z= 0.306 Chirality : 0.038 0.245 6935 Planarity : 0.004 0.052 2985 Dihedral : 14.333 179.550 14099 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 9.02 % 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: -1.14 (0.22), residues: 1470 helix: 0.48 (0.23), residues: 556 sheet: 0.04 (0.34), residues: 227 loop : -2.13 (0.22), residues: 687 *********************** 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 261 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 171 time to evaluate : 1.902 Fit side-chains revert: symmetry clash outliers start: 90 outliers final: 72 residues processed: 249 average time/residue: 1.3904 time to fit residues: 418.4894 Evaluate side-chains 241 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 169 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 68 residues processed: 5 average time/residue: 0.3492 time to fit residues: 5.3336 ------------------------------------------------------------------------------- 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: 0.1980 chunk 208 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 20 GLN ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 36076 Z= 0.133 Angle : 0.551 8.281 53953 Z= 0.288 Chirality : 0.035 0.229 6935 Planarity : 0.004 0.063 2985 Dihedral : 14.287 178.980 14099 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % 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: -1.00 (0.22), residues: 1470 helix: 0.61 (0.23), residues: 555 sheet: 0.08 (0.34), residues: 232 loop : -2.07 (0.22), residues: 683 *********************** 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 250 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 175 time to evaluate : 2.017 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 69 residues processed: 244 average time/residue: 1.4278 time to fit residues: 421.2058 Evaluate side-chains 241 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 172 time to evaluate : 2.221 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 66 residues processed: 4 average time/residue: 1.1885 time to fit residues: 8.4429 ------------------------------------------------------------------------------- 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: 0.9990 chunk 111 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 36076 Z= 0.183 Angle : 0.550 8.299 53953 Z= 0.287 Chirality : 0.036 0.232 6935 Planarity : 0.004 0.076 2985 Dihedral : 14.207 179.097 14099 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 7.01 % 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: -0.90 (0.22), residues: 1470 helix: 0.68 (0.23), residues: 560 sheet: 0.16 (0.34), residues: 232 loop : -2.04 (0.22), residues: 678 ********************** 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 244 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 174 time to evaluate : 2.149 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 67 residues processed: 243 average time/residue: 1.3844 time to fit residues: 406.3684 Evaluate side-chains 239 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 172 time to evaluate : 1.998 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 66 residues processed: 1 average time/residue: 0.4538 time to fit residues: 2.7791 ------------------------------------------------------------------------------- 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: 4.9990 chunk 180 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 40 GLN p 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.138517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.123182 restraints weight = 37370.380| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 0.23 r_work: 0.3230 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 36076 Z= 0.234 Angle : 0.573 8.276 53953 Z= 0.297 Chirality : 0.037 0.238 6935 Planarity : 0.004 0.051 2985 Dihedral : 14.210 179.398 14099 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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: -0.91 (0.22), residues: 1470 helix: 0.67 (0.23), residues: 561 sheet: 0.12 (0.34), residues: 230 loop : -2.02 (0.22), residues: 679 =============================================================================== Job complete usr+sys time: 6977.37 seconds wall clock time: 127 minutes 7.12 seconds (7627.12 seconds total)