Starting phenix.real_space_refine (version: dev) on Thu Dec 22 18:30:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/12_2022/6v3e_21034_updated.pdb" } resolution = 4.4 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= 0.002 sd= 0.033 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 "b TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 9": "NH1" <-> "NH2" Residue "b ASP 10": "OD1" <-> "OD2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 37": "NH1" <-> "NH2" Residue "b ARG 76": "NH1" <-> "NH2" Residue "b ARG 83": "NH1" <-> "NH2" Residue "b GLU 84": "OE1" <-> "OE2" Residue "b ARG 88": "NH1" <-> "NH2" Residue "b TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 134": "NH1" <-> "NH2" Residue "b ARG 141": "NH1" <-> "NH2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b ARG 148": "NH1" <-> "NH2" Residue "b GLU 171": "OE1" <-> "OE2" Residue "b ASP 190": "OD1" <-> "OD2" Residue "b ASP 196": "OD1" <-> "OD2" Residue "b ASP 199": "OD1" <-> "OD2" Residue "b ARG 210": "NH1" <-> "NH2" Residue "b TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c ARG 108": "NH1" <-> "NH2" Residue "c ARG 114": "NH1" <-> "NH2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 132": "NH1" <-> "NH2" Residue "c ARG 136": "NH1" <-> "NH2" Residue "c ARG 143": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c ARG 188": "NH1" <-> "NH2" Residue "c ARG 204": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d GLU 15": "OE1" <-> "OE2" Residue "d ARG 46": "NH1" <-> "NH2" Residue "d ARG 58": "NH1" <-> "NH2" Residue "d ARG 64": "NH1" <-> "NH2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 97": "OE1" <-> "OE2" Residue "d ARG 106": "NH1" <-> "NH2" Residue "d ARG 113": "NH1" <-> "NH2" Residue "d ARG 123": "NH1" <-> "NH2" Residue "d ARG 130": "NH1" <-> "NH2" Residue "d GLU 204": "OE1" <-> "OE2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 53": "NH1" <-> "NH2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e ARG 144": "NH1" <-> "NH2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "f ASP 41": "OD1" <-> "OD2" Residue "f ASP 72": "OD1" <-> "OD2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f GLU 76": "OE1" <-> "OE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "g ARG 10": "NH1" <-> "NH2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ASP 106": "OD1" <-> "OD2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 68": "OE1" <-> "OE2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "h ARG 118": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i GLU 108": "OE1" <-> "OE2" Residue "i ARG 122": "NH1" <-> "NH2" Residue "j ARG 5": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "j TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "k ARG 13": "NH1" <-> "NH2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "k ARG 36": "NH1" <-> "NH2" Residue "k PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 82": "OD1" <-> "OD2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k ASP 111": "OD1" <-> "OD2" Residue "l GLU 17": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 31": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 54": "NH1" <-> "NH2" Residue "l GLU 62": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 99": "NH1" <-> "NH2" Residue "l ASP 103": "OD1" <-> "OD2" Residue "m ARG 3": "NH1" <-> "NH2" Residue "m TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ASP 49": "OD1" <-> "OD2" Residue "m ARG 57": "NH1" <-> "NH2" Residue "m ARG 79": "NH1" <-> "NH2" Residue "m ARG 98": "NH1" <-> "NH2" Residue "m ARG 101": "NH1" <-> "NH2" Residue "m ARG 107": "NH1" <-> "NH2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "n ARG 59": "NH1" <-> "NH2" Residue "n ARG 61": "NH1" <-> "NH2" Residue "o ARG 58": "NH1" <-> "NH2" Residue "o ARG 64": "NH1" <-> "NH2" Residue "p ARG 46": "NH1" <-> "NH2" Residue "p GLU 87": "OE1" <-> "OE2" Residue "q ARG 40": "NH1" <-> "NH2" Residue "q ARG 41": "NH1" <-> "NH2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 27": "OD1" <-> "OD2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "r ARG 43": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ASP 72": "OD1" <-> "OD2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s ARG 28": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t ARG 18": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 34": "NH1" <-> "NH2" Residue "t ARG 78": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 50850 Number of models: 1 Model: "" Number of chains: 20 Chain: "sN" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 109, 'rna2p_pyr': 84, 'rna3p': 8, 'rna3p_pur': 754, 'rna3p_pyr': 572} Link IDs: {'rna2p': 193, 'rna3p': 1334} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" 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: "f" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 793 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "g" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1047 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" 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: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "q" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 630 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 438 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Time building chain proxies: 28.48, per 1000 atoms: 0.56 Number of scatterers: 50850 At special positions: 0 Unit cell: (139.384, 191.52, 256.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 1527 15.00 O 13879 8.00 N 9466 7.00 C 25917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS l 34 " - pdb=" SG CYS l 53 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 28.76 Conformation dependent library (CDL) restraints added in 3.3 seconds 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 20 sheets defined 38.7% alpha, 15.8% beta 467 base pairs and 777 stacking pairs defined. Time for finding SS restraints: 25.16 Creating SS restraints... Processing helix chain 'b' and resid 9 through 14 Processing helix chain 'b' and resid 45 through 65 Proline residue: b 50 - end of helix removed outlier: 3.966A pdb=" N LYS b 65 " --> pdb=" O GLN b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 89 removed outlier: 4.180A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU b 84 " --> pdb=" O ASN b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 123 removed outlier: 3.979A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER b 123 " --> pdb=" O LEU b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 149 removed outlier: 3.535A pdb=" N ARG b 148 " --> pdb=" O GLU b 144 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER b 149 " --> pdb=" O LYS b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 181 Processing helix chain 'b' and resid 209 through 226 removed outlier: 4.141A pdb=" N GLY b 226 " --> pdb=" O ALA b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 11 No H-bonds generated for 'chain 'c' and resid 9 through 11' Processing helix chain 'c' and resid 29 through 46 removed outlier: 3.709A pdb=" N LYS c 35 " --> pdb=" O GLU c 31 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS c 45 " --> pdb=" O GLU c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 50 No H-bonds generated for 'chain 'c' and resid 48 through 50' Processing helix chain 'c' and resid 73 through 76 No H-bonds generated for 'chain 'c' and resid 73 through 76' Processing helix chain 'c' and resid 82 through 94 Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.938A pdb=" N LYS c 126 " --> pdb=" O SER c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 143 Processing helix chain 'c' and resid 157 through 159 No H-bonds generated for 'chain 'c' and resid 157 through 159' Processing helix chain 'c' and resid 210 through 214 Processing helix chain 'd' and resid 9 through 15 removed outlier: 3.523A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 32 removed outlier: 3.589A pdb=" N THR d 32 " --> pdb=" O PHE d 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 28 through 32' Processing helix chain 'd' and resid 52 through 67 removed outlier: 3.596A pdb=" N ARG d 64 " --> pdb=" O LYS d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 83 Processing helix chain 'd' and resid 88 through 97 removed outlier: 3.959A pdb=" N LEU d 92 " --> pdb=" O THR d 88 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU d 93 " --> pdb=" O GLY d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 107 Processing helix chain 'd' and resid 113 through 121 Processing helix chain 'd' and resid 155 through 166 removed outlier: 3.807A pdb=" N ALA d 160 " --> pdb=" O ARG d 156 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN d 166 " --> pdb=" O GLU d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 206 Processing helix chain 'e' and resid 55 through 67 Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.957A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 144 removed outlier: 3.841A pdb=" N ARG e 144 " --> pdb=" O PHE e 140 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 156 Processing helix chain 'e' and resid 160 through 163 No H-bonds generated for 'chain 'e' and resid 160 through 163' Processing helix chain 'f' and resid 12 through 18 removed outlier: 4.283A pdb=" N ASP f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL f 18 " --> pdb=" O SER f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 22 through 28 removed outlier: 4.753A pdb=" N ILE f 26 " --> pdb=" O VAL f 22 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 32 No H-bonds generated for 'chain 'f' and resid 30 through 32' Processing helix chain 'f' and resid 71 through 80 removed outlier: 4.679A pdb=" N LEU f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR f 80 " --> pdb=" O GLU f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 30 Processing helix chain 'g' and resid 36 through 53 removed outlier: 3.580A pdb=" N GLU g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 69 removed outlier: 4.445A pdb=" N GLU g 63 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR g 64 " --> pdb=" O GLU g 60 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL g 69 " --> pdb=" O THR g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 110 removed outlier: 3.895A pdb=" N ASP g 106 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 129 Processing helix chain 'g' and resid 133 through 137 Processing helix chain 'h' and resid 7 through 19 Processing helix chain 'h' and resid 31 through 43 Processing helix chain 'h' and resid 96 through 99 Processing helix chain 'h' and resid 114 through 120 Processing helix chain 'i' and resid 33 through 36 No H-bonds generated for 'chain 'i' and resid 33 through 36' Processing helix chain 'i' and resid 40 through 52 removed outlier: 3.724A pdb=" N VAL i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 70 through 88 Processing helix chain 'i' and resid 90 through 99 Proline residue: i 94 - end of helix removed outlier: 3.659A pdb=" N ARG i 97 " --> pdb=" O PRO i 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN i 98 " --> pdb=" O VAL i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 15 through 32 removed outlier: 3.786A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 89 removed outlier: 4.063A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 57 Processing helix chain 'k' and resid 59 through 76 removed outlier: 3.871A pdb=" N VAL k 64 " --> pdb=" O PHE k 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA k 69 " --> pdb=" O ALA k 65 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA k 72 " --> pdb=" O VAL k 68 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 94 through 102 removed outlier: 3.675A pdb=" N ALA k 101 " --> pdb=" O ARG k 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL k 102 " --> pdb=" O ALA k 98 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 Processing helix chain 'm' and resid 15 through 21 removed outlier: 3.650A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 37 Processing helix chain 'm' and resid 50 through 62 removed outlier: 4.050A pdb=" N ALA m 55 " --> pdb=" O ALA m 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU m 59 " --> pdb=" O ALA m 55 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 83 removed outlier: 3.555A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 94 removed outlier: 5.147A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 19 Processing helix chain 'n' and resid 21 through 32 Processing helix chain 'n' and resid 38 through 50 Processing helix chain 'n' and resid 53 through 55 No H-bonds generated for 'chain 'n' and resid 53 through 55' Processing helix chain 'n' and resid 57 through 59 No H-bonds generated for 'chain 'n' and resid 57 through 59' Processing helix chain 'n' and resid 81 through 90 removed outlier: 3.523A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 15 Processing helix chain 'o' and resid 25 through 44 removed outlier: 4.168A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS o 44 " --> pdb=" O GLN o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 73 removed outlier: 3.583A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 85 Processing helix chain 'p' and resid 72 through 80 Processing helix chain 'p' and resid 87 through 99 Processing helix chain 'r' and resid 26 through 32 removed outlier: 3.989A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 45 No H-bonds generated for 'chain 'r' and resid 42 through 45' Processing helix chain 'r' and resid 49 through 64 Processing helix chain 's' and resid 13 through 25 Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 64 through 66 No H-bonds generated for 'chain 's' and resid 64 through 66' Processing helix chain 's' and resid 71 through 74 removed outlier: 3.582A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 71 through 74' Processing helix chain 't' and resid 5 through 41 removed outlier: 3.530A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 64 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 69 through 86 removed outlier: 3.694A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'b' and resid 69 through 72 removed outlier: 7.694A pdb=" N ALA b 162 " --> pdb=" O LEU b 70 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N VAL b 72 " --> pdb=" O ALA b 162 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE b 164 " --> pdb=" O VAL b 72 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL b 165 " --> pdb=" O PRO b 184 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE b 186 " --> pdb=" O VAL b 165 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR b 200 " --> pdb=" O GLY b 187 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL b 189 " --> pdb=" O TYR b 200 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE b 202 " --> pdb=" O VAL b 189 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'b' and resid 33 through 36 removed outlier: 7.300A pdb=" N ILE b 42 " --> pdb=" O PHE b 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'c' and resid 99 through 105 removed outlier: 6.433A pdb=" N ALA c 64 " --> pdb=" O GLN c 100 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER c 102 " --> pdb=" O ALA c 64 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL c 66 " --> pdb=" O SER c 102 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN c 104 " --> pdb=" O VAL c 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE c 68 " --> pdb=" O ASN c 104 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'c' and resid 164 through 171 Processing sheet with id= E, first strand: chain 'd' and resid 130 through 132 removed outlier: 4.563A pdb=" N ILE d 125 " --> pdb=" O VAL d 132 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'e' and resid 70 through 72 removed outlier: 6.249A pdb=" N VAL e 37 " --> pdb=" O LEU e 14 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU e 14 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLY e 39 " --> pdb=" O GLU e 12 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU e 12 " --> pdb=" O GLY e 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'e' and resid 84 through 88 Processing sheet with id= H, first strand: chain 'f' and resid 88 through 92 removed outlier: 3.676A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE f 60 " --> pdb=" O LEU f 8 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU f 61 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP f 41 " --> pdb=" O LEU f 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'g' and resid 74 through 76 removed outlier: 3.904A pdb=" N LYS g 76 " --> pdb=" O VAL g 87 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL g 87 " --> pdb=" O LYS g 76 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.783A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'h' and resid 76 through 78 removed outlier: 7.141A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE h 129 " --> pdb=" O ILE h 102 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE h 102 " --> pdb=" O PHE h 129 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'i' and resid 4 through 9 Processing sheet with id= M, first strand: chain 'j' and resid 96 through 100 removed outlier: 4.652A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'j' and resid 45 through 52 Processing sheet with id= O, first strand: chain 'k' and resid 82 through 86 Processing sheet with id= P, first strand: chain 'l' and resid 95 through 97 removed outlier: 6.460A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'p' and resid 20 through 27 removed outlier: 3.857A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL p 39 " --> pdb=" O ARG p 53 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ARG p 53 " --> pdb=" O VAL p 39 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'q' and resid 74 through 76 removed outlier: 16.839A pdb=" N THR q 8 " --> pdb=" O ARG q 29 " (cutoff:3.500A) removed outlier: 13.312A pdb=" N ARG q 29 " --> pdb=" O THR q 8 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR q 10 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU q 27 " --> pdb=" O THR q 10 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL q 23 " --> pdb=" O VAL q 14 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'q' and resid 59 through 61 removed outlier: 6.541A pdb=" N THR q 61 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL q 79 " --> pdb=" O THR q 61 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 's' and resid 30 through 33 removed outlier: 7.403A pdb=" N THR s 48 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N THR s 33 " --> pdb=" O THR s 48 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER s 50 " --> pdb=" O THR s 33 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1171 hydrogen bonds 1822 hydrogen bond angles 0 basepair planarities 467 basepair parallelities 777 stacking parallelities Total time for adding SS restraints: 54.25 Time building geometry restraints manager: 30.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4949 1.31 - 1.44: 23893 1.44 - 1.56: 23022 1.56 - 1.69: 3054 1.69 - 1.82: 111 Bond restraints: 55029 Sorted by residual: bond pdb=" N6 MA6sN1516 " pdb=" C9 MA6sN1516 " ideal model delta sigma weight residual 1.522 1.443 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" N6 MA6sN1515 " pdb=" C9 MA6sN1515 " ideal model delta sigma weight residual 1.522 1.444 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C VAL b 49 " pdb=" N PRO b 50 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.20e-02 6.94e+03 6.44e+00 bond pdb=" P 2MGsN 963 " pdb=" OP1 2MGsN 963 " ideal model delta sigma weight residual 1.545 1.509 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" P 2MGsN1204 " pdb=" OP1 2MGsN1204 " ideal model delta sigma weight residual 1.545 1.510 0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 55024 not shown) Histogram of bond angle deviations from ideal: 99.50 - 107.26: 9505 107.26 - 115.01: 35970 115.01 - 122.76: 26914 122.76 - 130.52: 8902 130.52 - 138.27: 598 Bond angle restraints: 81889 Sorted by residual: angle pdb=" C1' MA6sN1516 " pdb=" N9 MA6sN1516 " pdb=" C4 MA6sN1516 " ideal model delta sigma weight residual 112.44 124.96 -12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" C1' MA6sN1515 " pdb=" N9 MA6sN1515 " pdb=" C4 MA6sN1515 " ideal model delta sigma weight residual 112.44 124.72 -12.28 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C3' UsN 989 " pdb=" O3' UsN 989 " pdb=" P GsN 990 " ideal model delta sigma weight residual 120.20 125.65 -5.45 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C3' UsN1123 " pdb=" O3' UsN1123 " pdb=" P GsN1124 " ideal model delta sigma weight residual 120.20 125.35 -5.15 1.50e+00 4.44e-01 1.18e+01 angle pdb=" C1' 2MGsN1204 " pdb=" N9 2MGsN1204 " pdb=" C4 2MGsN1204 " ideal model delta sigma weight residual 109.53 119.51 -9.98 3.00e+00 1.11e-01 1.11e+01 ... (remaining 81884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 28722 35.97 - 71.95: 838 71.95 - 107.92: 71 107.92 - 143.90: 3 143.90 - 179.87: 19 Dihedral angle restraints: 29653 sinusoidal: 23031 harmonic: 6622 Sorted by residual: dihedral pdb=" O4' CsN 326 " pdb=" C1' CsN 326 " pdb=" N1 CsN 326 " pdb=" C2 CsN 326 " ideal model delta sinusoidal sigma weight residual 200.00 38.05 161.95 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" O4' CsN 717 " pdb=" C1' CsN 717 " pdb=" N1 CsN 717 " pdb=" C2 CsN 717 " ideal model delta sinusoidal sigma weight residual 200.00 41.10 158.90 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' UsN 419 " pdb=" C1' UsN 419 " pdb=" N1 UsN 419 " pdb=" C2 UsN 419 " ideal model delta sinusoidal sigma weight residual 200.00 43.61 156.39 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 29650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 9838 0.057 - 0.113: 493 0.113 - 0.170: 57 0.170 - 0.226: 2 0.226 - 0.283: 2 Chirality restraints: 10392 Sorted by residual: chirality pdb=" C1* PSUsN 513 " pdb=" O4* PSUsN 513 " pdb=" C2* PSUsN 513 " pdb=" C5 PSUsN 513 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3' UsN1123 " pdb=" C4' UsN1123 " pdb=" O3' UsN1123 " pdb=" C2' UsN1123 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3' UsN 989 " pdb=" C4' UsN 989 " pdb=" O3' UsN 989 " pdb=" C2' UsN 989 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 10389 not shown) Planarity restraints: 4722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MGsN 963 " 0.040 2.00e-02 2.50e+03 5.80e-01 7.56e+03 pdb=" C4' 2MGsN 963 " 0.435 2.00e-02 2.50e+03 pdb=" O4' 2MGsN 963 " 0.635 2.00e-02 2.50e+03 pdb=" C3' 2MGsN 963 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MGsN 963 " -0.587 2.00e-02 2.50e+03 pdb=" C2' 2MGsN 963 " -0.202 2.00e-02 2.50e+03 pdb=" O2' 2MGsN 963 " 0.928 2.00e-02 2.50e+03 pdb=" C1' 2MGsN 963 " 0.225 2.00e-02 2.50e+03 pdb=" N9 2MGsN 963 " -0.883 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGsN1204 " 0.028 2.00e-02 2.50e+03 5.65e-01 7.19e+03 pdb=" C4' 2MGsN1204 " 0.434 2.00e-02 2.50e+03 pdb=" O4' 2MGsN1204 " 0.633 2.00e-02 2.50e+03 pdb=" C3' 2MGsN1204 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 2MGsN1204 " -0.553 2.00e-02 2.50e+03 pdb=" C2' 2MGsN1204 " -0.218 2.00e-02 2.50e+03 pdb=" O2' 2MGsN1204 " 0.894 2.00e-02 2.50e+03 pdb=" C1' 2MGsN1204 " 0.229 2.00e-02 2.50e+03 pdb=" N9 2MGsN1204 " -0.858 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MGsN 524 " -0.027 2.00e-02 2.50e+03 5.63e-01 7.13e+03 pdb=" C4' 7MGsN 524 " -0.431 2.00e-02 2.50e+03 pdb=" O4' 7MGsN 524 " -0.627 2.00e-02 2.50e+03 pdb=" C3' 7MGsN 524 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 7MGsN 524 " 0.550 2.00e-02 2.50e+03 pdb=" C2' 7MGsN 524 " 0.218 2.00e-02 2.50e+03 pdb=" O2' 7MGsN 524 " -0.893 2.00e-02 2.50e+03 pdb=" C1' 7MGsN 524 " -0.230 2.00e-02 2.50e+03 pdb=" N9 7MGsN 524 " 0.853 2.00e-02 2.50e+03 ... (remaining 4719 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1078 2.61 - 3.18: 41212 3.18 - 3.76: 100087 3.76 - 4.33: 130223 4.33 - 4.90: 177183 Nonbonded interactions: 449783 Sorted by model distance: nonbonded pdb=" O2 UsN 202 " pdb=" O6 GsN 208 " model vdw 2.039 2.432 nonbonded pdb=" N1 AsN 75 " pdb=" O6 GsN 92 " model vdw 2.122 2.496 nonbonded pdb=" O2 UsN 602 " pdb=" O6 GsN 630 " model vdw 2.130 2.432 nonbonded pdb=" N7 GsN1157 " pdb=" N2 GsN1179 " model vdw 2.136 2.560 nonbonded pdb=" N2 GsN 503 " pdb=" O2 CsN 522 " model vdw 2.140 2.496 ... (remaining 449778 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: 5 Type Number sf(0) Gaussians P 1527 5.49 5 S 61 5.16 5 C 25917 2.51 5 N 9466 2.21 5 O 13879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 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: 0.050 Extract box with map and model: 30.620 Check model and map are aligned: 0.770 Convert atoms to be neutral: 0.440 Process input model: 184.080 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 : 0.002 0.079 55029 Z= 0.114 Angle : 0.452 12.519 81889 Z= 0.248 Chirality : 0.027 0.283 10392 Planarity : 0.017 0.580 4722 Dihedral : 14.342 179.874 25380 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.05 % 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: -1.40 (0.16), residues: 2273 helix: -0.91 (0.15), residues: 881 sheet: 0.30 (0.27), residues: 373 loop : -1.32 (0.18), residues: 1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 544 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 545 average time/residue: 0.7120 time to fit residues: 608.6926 Evaluate side-chains 310 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 3.522 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5577 time to fit residues: 4.6217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 341 optimal weight: 0.1980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 5 ASN ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN b 120 GLN b 122 GLN b 180 ASN ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN c 88 GLN ** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN d 73 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 GLN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 52 ASN ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 4 GLN h 38 ASN h 98 GLN i 73 GLN j 56 HIS j 58 ASN ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 82 ASN o 42 HIS o 50 HIS q 32 HIS ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 HIS s 83 HIS t 13 GLN t 21 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 55029 Z= 0.226 Angle : 0.630 16.094 81889 Z= 0.333 Chirality : 0.032 0.365 10392 Planarity : 0.006 0.113 4722 Dihedral : 14.654 179.910 20875 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.05 % 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: -0.55 (0.17), residues: 2273 helix: 0.07 (0.17), residues: 897 sheet: 0.53 (0.27), residues: 372 loop : -1.05 (0.19), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 392 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.6779 time to fit residues: 433.5989 Evaluate side-chains 286 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.059 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 0.5980 chunk 369 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 274 optimal weight: 0.9980 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 17 HIS b 91 GLN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 3 GLN c 28 GLN ** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN i 73 GLN i 124 GLN j 23 GLN j 56 HIS ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 21 HIS k 37 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 77 HIS ** r 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 61 GLN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 55029 Z= 0.315 Angle : 0.761 13.701 81889 Z= 0.397 Chirality : 0.038 0.448 10392 Planarity : 0.007 0.129 4722 Dihedral : 15.816 179.948 20875 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 30.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.65 (0.17), residues: 2273 helix: -0.14 (0.17), residues: 864 sheet: 0.27 (0.27), residues: 379 loop : -0.86 (0.19), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 341 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 342 average time/residue: 0.6616 time to fit residues: 371.4161 Evaluate side-chains 265 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 3.218 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4211 time to fit residues: 4.3336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 343 optimal weight: 2.9990 chunk 363 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN h 98 GLN ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 52 GLN r 61 GLN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 55029 Z= 0.180 Angle : 0.610 13.981 81889 Z= 0.327 Chirality : 0.033 0.451 10392 Planarity : 0.006 0.121 4722 Dihedral : 15.584 179.835 20875 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.00 % 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: -0.31 (0.17), residues: 2273 helix: 0.32 (0.17), residues: 878 sheet: 0.27 (0.27), residues: 362 loop : -0.77 (0.20), residues: 1033 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.6377 time to fit residues: 380.2582 Evaluate side-chains 278 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 270 optimal weight: 0.0270 chunk 149 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 326 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 41 HIS ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN ** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 GLN ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 55029 Z= 0.175 Angle : 0.598 13.787 81889 Z= 0.321 Chirality : 0.033 0.442 10392 Planarity : 0.005 0.122 4722 Dihedral : 15.515 179.564 20875 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.05 % 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: -0.16 (0.18), residues: 2273 helix: 0.53 (0.17), residues: 886 sheet: 0.28 (0.27), residues: 360 loop : -0.74 (0.20), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 352 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.6394 time to fit residues: 373.7308 Evaluate side-chains 274 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 10.0000 chunk 327 optimal weight: 0.0570 chunk 71 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 363 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 0.6980 overall best weight: 3.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 HIS c 28 GLN c 88 GLN ** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN m 52 GLN n 54 ASN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 55029 Z= 0.252 Angle : 0.684 13.646 81889 Z= 0.361 Chirality : 0.036 0.475 10392 Planarity : 0.006 0.123 4722 Dihedral : 15.976 179.446 20875 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.00 % 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: -0.46 (0.17), residues: 2273 helix: 0.30 (0.17), residues: 882 sheet: -0.01 (0.26), residues: 366 loop : -0.86 (0.20), residues: 1025 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.6533 time to fit residues: 365.3499 Evaluate side-chains 268 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 205 optimal weight: 0.5980 chunk 306 optimal weight: 9.9990 chunk 203 optimal weight: 0.7980 chunk 362 optimal weight: 0.6980 chunk 226 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN ** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 HIS ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN h 38 ASN ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 55029 Z= 0.145 Angle : 0.593 13.531 81889 Z= 0.317 Chirality : 0.033 0.443 10392 Planarity : 0.005 0.120 4722 Dihedral : 15.685 179.630 20875 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.00 % 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: -0.10 (0.18), residues: 2273 helix: 0.71 (0.18), residues: 869 sheet: 0.07 (0.27), residues: 356 loop : -0.72 (0.20), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.6259 time to fit residues: 372.6093 Evaluate side-chains 278 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 179 optimal weight: 0.0870 chunk 33 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 41 HIS b 44 ASN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 HIS ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 ASN p 36 GLN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.067 55029 Z= 0.425 Angle : 0.911 12.982 81889 Z= 0.467 Chirality : 0.045 0.540 10392 Planarity : 0.008 0.126 4722 Dihedral : 17.073 179.755 20875 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 40.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.15 (0.17), residues: 2273 helix: -0.39 (0.17), residues: 853 sheet: -0.39 (0.27), residues: 351 loop : -1.11 (0.19), residues: 1069 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.6419 time to fit residues: 343.3064 Evaluate side-chains 250 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 3.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 7.9990 chunk 347 optimal weight: 9.9990 chunk 316 optimal weight: 0.2980 chunk 337 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 319 optimal weight: 4.9990 chunk 336 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN ** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 28 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 GLN s 14 HIS t 21 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 55029 Z= 0.198 Angle : 0.661 13.176 81889 Z= 0.350 Chirality : 0.036 0.496 10392 Planarity : 0.006 0.122 4722 Dihedral : 16.465 179.454 20875 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.68 (0.17), residues: 2273 helix: 0.26 (0.17), residues: 853 sheet: -0.23 (0.27), residues: 355 loop : -1.05 (0.19), residues: 1065 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 341 average time/residue: 0.6533 time to fit residues: 371.4952 Evaluate side-chains 264 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 8.9990 chunk 357 optimal weight: 30.0000 chunk 217 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 374 optimal weight: 7.9990 chunk 344 optimal weight: 1.9990 chunk 298 optimal weight: 0.3980 chunk 30 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 91 GLN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN ** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 GLN ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN m 52 GLN ** q 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 55029 Z= 0.163 Angle : 0.616 13.381 81889 Z= 0.327 Chirality : 0.034 0.468 10392 Planarity : 0.006 0.121 4722 Dihedral : 16.074 179.915 20875 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.11 % 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: -0.47 (0.18), residues: 2273 helix: 0.44 (0.17), residues: 863 sheet: -0.14 (0.27), residues: 360 loop : -0.94 (0.20), residues: 1050 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4546 Ramachandran restraints generated. 2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 344 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 345 average time/residue: 0.6343 time to fit residues: 363.3230 Evaluate side-chains 274 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 3.378 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5065 time to fit residues: 4.4119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 20.0000 chunk 317 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 275 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 ASN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.063613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.045839 restraints weight = 477671.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.045041 restraints weight = 419301.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.045121 restraints weight = 323916.327| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 55029 Z= 0.454 Angle : 0.953 12.743 81889 Z= 0.485 Chirality : 0.047 0.568 10392 Planarity : 0.008 0.125 4722 Dihedral : 17.489 178.908 20875 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 44.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.49 (0.17), residues: 2273 helix: -0.59 (0.16), residues: 862 sheet: -0.78 (0.26), residues: 367 loop : -1.30 (0.19), residues: 1044 =============================================================================== Job complete usr+sys time: 8621.84 seconds wall clock time: 160 minutes 16.98 seconds (9616.98 seconds total)