Starting phenix.real_space_refine on Mon Mar 25 19:11:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/03_2024/6v3e_21034_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/03_2024/6v3e_21034.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/03_2024/6v3e_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_21034/03_2024/6v3e_21034_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/03_2024/6v3e_21034_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/03_2024/6v3e_21034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/03_2024/6v3e_21034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/03_2024/6v3e_21034_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/03_2024/6v3e_21034_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 26.01, per 1000 atoms: 0.51 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: 27.52 Conformation dependent library (CDL) restraints added in 3.8 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: 28.91 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: 45.03 Time building geometry restraints manager: 29.27 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 1.517 1.443 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" N6 MA6sN1515 " pdb=" C9 MA6sN1515 " ideal model delta sigma weight residual 1.517 1.444 0.073 2.00e-02 2.50e+03 1.34e+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=" N3 UR3sN1495 " pdb=" C3U UR3sN1495 " ideal model delta sigma weight residual 1.490 1.442 0.048 2.00e-02 2.50e+03 5.65e+00 bond pdb=" CA CYS l 53 " pdb=" CB CYS l 53 " ideal model delta sigma weight residual 1.532 1.563 -0.031 1.82e-02 3.02e+03 2.90e+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' 2MGsN 963 " pdb=" N9 2MGsN 963 " pdb=" C8 2MGsN 963 " ideal model delta sigma weight residual 110.07 132.65 -22.58 3.00e+00 1.11e-01 5.66e+01 angle pdb=" C1' 2MGsN1204 " pdb=" N9 2MGsN1204 " pdb=" C8 2MGsN1204 " ideal model delta sigma weight residual 110.07 132.15 -22.08 3.00e+00 1.11e-01 5.42e+01 angle pdb=" C1' 2MGsN 963 " pdb=" N9 2MGsN 963 " pdb=" C4 2MGsN 963 " ideal model delta sigma weight residual 138.70 119.04 19.66 3.00e+00 1.11e-01 4.29e+01 angle pdb=" C1' 2MGsN1204 " pdb=" N9 2MGsN1204 " pdb=" C4 2MGsN1204 " ideal model delta sigma weight residual 138.70 119.51 19.19 3.00e+00 1.11e-01 4.09e+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 ... (remaining 81884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 31193 35.97 - 71.95: 3554 71.95 - 107.92: 391 107.92 - 143.90: 3 143.90 - 179.87: 19 Dihedral angle restraints: 35160 sinusoidal: 28538 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 35157 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 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: 8.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 29.270 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 172.650 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 0.074 55029 Z= 0.111 Angle : 0.467 22.580 81889 Z= 0.251 Chirality : 0.027 0.283 10392 Planarity : 0.017 0.580 4722 Dihedral : 22.687 179.874 30887 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.93 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 98 HIS 0.007 0.001 HIS b 96 PHE 0.008 0.001 PHE n 42 TYR 0.010 0.001 TYR b 93 ARG 0.004 0.000 ARG b 210 *********************** 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 : 2.894 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 REVERT: b 113 ILE cc_start: 0.7129 (tp) cc_final: 0.6899 (tp) REVERT: b 143 MET cc_start: 0.5726 (mmp) cc_final: 0.5202 (mmt) REVERT: b 170 HIS cc_start: 0.4249 (t70) cc_final: 0.3785 (t-170) REVERT: c 43 LEU cc_start: 0.8877 (mt) cc_final: 0.8667 (mt) REVERT: c 110 ASP cc_start: 0.9119 (m-30) cc_final: 0.7720 (t0) REVERT: c 123 GLN cc_start: 0.9264 (mm110) cc_final: 0.8799 (mm-40) REVERT: c 181 ASP cc_start: 0.8896 (t0) cc_final: 0.8496 (p0) REVERT: d 20 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8492 (mm-40) REVERT: d 90 GLU cc_start: 0.8975 (pt0) cc_final: 0.8401 (pm20) REVERT: f 3 HIS cc_start: 0.8174 (m-70) cc_final: 0.7946 (m-70) REVERT: g 61 PHE cc_start: 0.8891 (t80) cc_final: 0.8592 (t80) REVERT: h 41 GLN cc_start: 0.9334 (tt0) cc_final: 0.9079 (tt0) REVERT: h 60 LEU cc_start: 0.9384 (tp) cc_final: 0.9051 (tp) REVERT: h 93 LEU cc_start: 0.8796 (mt) cc_final: 0.8537 (mt) REVERT: h 114 ASP cc_start: 0.9006 (p0) cc_final: 0.8704 (p0) REVERT: i 60 ASP cc_start: 0.8532 (m-30) cc_final: 0.7090 (m-30) REVERT: i 62 TYR cc_start: 0.8649 (t80) cc_final: 0.8241 (t80) REVERT: i 105 ASP cc_start: 0.7569 (t0) cc_final: 0.7180 (t0) REVERT: j 66 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6521 (tm-30) REVERT: j 78 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8735 (pp30) REVERT: l 75 GLN cc_start: 0.8464 (mm110) cc_final: 0.8121 (pm20) REVERT: l 96 HIS cc_start: 0.8188 (m-70) cc_final: 0.7944 (m90) REVERT: m 54 ASP cc_start: 0.8107 (p0) cc_final: 0.7740 (p0) REVERT: m 69 LEU cc_start: 0.9426 (tp) cc_final: 0.8947 (tp) REVERT: m 81 MET cc_start: 0.8512 (mtt) cc_final: 0.8165 (mtt) REVERT: n 87 THR cc_start: 0.9042 (m) cc_final: 0.8796 (p) REVERT: n 92 ASP cc_start: 0.8803 (m-30) cc_final: 0.8252 (p0) REVERT: o 58 ARG cc_start: 0.9051 (ttt180) cc_final: 0.8742 (ttp-110) REVERT: o 59 MET cc_start: 0.9243 (mtt) cc_final: 0.8683 (mtm) REVERT: o 76 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8514 (pp20) REVERT: o 77 ARG cc_start: 0.9347 (mtm180) cc_final: 0.8551 (ttp-110) REVERT: p 98 LYS cc_start: 0.9616 (pptt) cc_final: 0.9366 (ptpp) REVERT: q 25 LEU cc_start: 0.9519 (tp) cc_final: 0.9057 (tp) REVERT: r 29 LEU cc_start: 0.6041 (mt) cc_final: 0.5182 (mt) REVERT: r 32 TYR cc_start: 0.7257 (m-80) cc_final: 0.6960 (m-80) REVERT: r 64 TYR cc_start: 0.8990 (t80) cc_final: 0.8421 (t80) REVERT: s 16 PHE cc_start: 0.9137 (t80) cc_final: 0.8766 (t80) REVERT: s 20 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8202 (mt-10) REVERT: s 40 ILE cc_start: 0.8285 (mt) cc_final: 0.7946 (mt) REVERT: s 41 LEU cc_start: 0.9113 (mm) cc_final: 0.8537 (mm) REVERT: s 44 PHE cc_start: 0.8955 (m-10) cc_final: 0.8633 (m-80) REVERT: s 65 HIS cc_start: 0.8128 (m-70) cc_final: 0.7538 (m90) outliers start: 1 outliers final: 1 residues processed: 545 average time/residue: 0.7132 time to fit residues: 607.1323 Evaluate side-chains 328 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 2.912 ------------------------------------------------------------------------------- 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: 10.0000 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: 9.9990 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 28 GLN c 88 GLN ** 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** f 94 HIS h 4 GLN h 38 ASN h 98 GLN i 73 GLN j 56 HIS j 58 ASN ** 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 o 75 HIS q 32 HIS ** r 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 83 HIS t 13 GLN t 21 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 55029 Z= 0.219 Angle : 0.604 13.280 81889 Z= 0.320 Chirality : 0.032 0.424 10392 Planarity : 0.006 0.126 4722 Dihedral : 23.458 179.958 26382 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.82 % 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: -0.57 (0.17), residues: 2273 helix: 0.04 (0.17), residues: 899 sheet: 0.56 (0.27), residues: 372 loop : -1.06 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 103 HIS 0.008 0.001 HIS q 48 PHE 0.019 0.002 PHE s 74 TYR 0.042 0.002 TYR n 73 ARG 0.023 0.001 ARG g 119 *********************** 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 406 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 3.056 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: c 110 ASP cc_start: 0.9098 (m-30) cc_final: 0.7801 (t0) REVERT: c 123 GLN cc_start: 0.9292 (mm110) cc_final: 0.8808 (mm-40) REVERT: c 187 MET cc_start: 0.9118 (tpp) cc_final: 0.8900 (tpp) REVERT: d 20 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8233 (mp-120) REVERT: d 100 LEU cc_start: 0.9189 (tp) cc_final: 0.8859 (tt) REVERT: d 107 MET cc_start: 0.8573 (tpt) cc_final: 0.8308 (tpp) REVERT: e 96 GLN cc_start: 0.7209 (pp30) cc_final: 0.6960 (pp30) REVERT: e 146 MET cc_start: 0.9279 (tpp) cc_final: 0.8986 (tpp) REVERT: f 54 ILE cc_start: 0.8418 (pt) cc_final: 0.8216 (tp) REVERT: g 70 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7962 (mmm-85) REVERT: h 27 MET cc_start: 0.8578 (pmm) cc_final: 0.8369 (pmm) REVERT: h 41 GLN cc_start: 0.9352 (tt0) cc_final: 0.8850 (tt0) REVERT: h 93 LEU cc_start: 0.8893 (mt) cc_final: 0.8551 (mt) REVERT: i 59 TYR cc_start: 0.9213 (m-80) cc_final: 0.8939 (m-80) REVERT: i 62 TYR cc_start: 0.8792 (t80) cc_final: 0.8267 (t80) REVERT: i 113 LYS cc_start: 0.9233 (mptt) cc_final: 0.8824 (mmtm) REVERT: j 47 GLU cc_start: 0.8695 (tt0) cc_final: 0.8461 (tt0) REVERT: j 78 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8763 (pp30) REVERT: k 116 PRO cc_start: 0.6763 (Cg_endo) cc_final: 0.6547 (Cg_exo) REVERT: l 75 GLN cc_start: 0.8518 (mm110) cc_final: 0.8132 (pm20) REVERT: l 96 HIS cc_start: 0.8055 (m-70) cc_final: 0.7767 (m90) REVERT: m 50 ASP cc_start: 0.7937 (t70) cc_final: 0.7672 (t0) REVERT: m 69 LEU cc_start: 0.9366 (tp) cc_final: 0.9077 (tp) REVERT: m 81 MET cc_start: 0.8682 (mtt) cc_final: 0.8284 (mtt) REVERT: m 100 GLN cc_start: 0.7291 (mp10) cc_final: 0.6984 (mp10) REVERT: n 20 TYR cc_start: 0.7986 (m-80) cc_final: 0.7780 (m-10) REVERT: n 84 LEU cc_start: 0.9517 (mt) cc_final: 0.9151 (mt) REVERT: n 92 ASP cc_start: 0.8834 (m-30) cc_final: 0.8317 (p0) REVERT: q 25 LEU cc_start: 0.9450 (tp) cc_final: 0.9084 (tp) REVERT: r 22 ASP cc_start: 0.6658 (p0) cc_final: 0.6439 (p0) REVERT: r 32 TYR cc_start: 0.7472 (m-80) cc_final: 0.7007 (m-80) REVERT: s 16 PHE cc_start: 0.9161 (t80) cc_final: 0.8597 (t80) REVERT: s 20 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8210 (mt-10) REVERT: s 41 LEU cc_start: 0.9192 (mm) cc_final: 0.8704 (mm) REVERT: s 65 HIS cc_start: 0.7781 (m-70) cc_final: 0.7295 (m90) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.6743 time to fit residues: 442.1889 Evaluate side-chains 305 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 3.007 ------------------------------------------------------------------------------- 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: 10.0000 chunk 284 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** b 170 HIS ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 20 GLN 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 i 73 GLN i 124 GLN j 23 GLN ** j 56 HIS ** 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** l 96 HIS ** 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 ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 55029 Z= 0.432 Angle : 0.961 12.834 81889 Z= 0.494 Chirality : 0.046 0.560 10392 Planarity : 0.009 0.140 4722 Dihedral : 24.482 178.554 26382 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 40.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.32 % Allowed : 9.31 % Favored : 90.38 % 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: -1.17 (0.17), residues: 2273 helix: -0.62 (0.16), residues: 845 sheet: -0.05 (0.26), residues: 382 loop : -1.08 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP g 103 HIS 0.011 0.003 HIS p 77 PHE 0.029 0.003 PHE n 42 TYR 0.031 0.003 TYR e 127 ARG 0.018 0.001 ARG g 79 *********************** 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 353 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 347 time to evaluate : 2.932 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: b 102 MET cc_start: 0.6868 (mtt) cc_final: 0.6557 (mtt) REVERT: b 179 LYS cc_start: 0.7347 (pptt) cc_final: 0.7114 (mmpt) REVERT: c 110 ASP cc_start: 0.8821 (m-30) cc_final: 0.7110 (t0) REVERT: c 123 GLN cc_start: 0.9256 (mm110) cc_final: 0.8951 (mp10) REVERT: d 4 TYR cc_start: 0.7860 (t80) cc_final: 0.7660 (t80) REVERT: d 74 PHE cc_start: 0.9079 (t80) cc_final: 0.8687 (t80) REVERT: d 94 LYS cc_start: 0.9629 (mtpt) cc_final: 0.9394 (mmtt) REVERT: d 206 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: e 96 GLN cc_start: 0.7573 (pp30) cc_final: 0.7316 (pp30) REVERT: f 6 ILE cc_start: 0.7500 (mp) cc_final: 0.7227 (mp) REVERT: f 62 MET cc_start: 0.6585 (mpp) cc_final: 0.6348 (mpp) REVERT: g 89 MET cc_start: 0.5427 (tpt) cc_final: 0.4996 (ttt) REVERT: g 101 MET cc_start: 0.6564 (ttp) cc_final: 0.6313 (ttp) REVERT: h 60 LEU cc_start: 0.9311 (tp) cc_final: 0.9099 (tp) REVERT: h 65 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7764 (mtpp) REVERT: h 84 LEU cc_start: 0.9653 (tp) cc_final: 0.9414 (tt) REVERT: h 87 TYR cc_start: 0.8853 (m-80) cc_final: 0.8314 (m-80) REVERT: h 93 LEU cc_start: 0.9068 (mt) cc_final: 0.8666 (mt) REVERT: h 125 GLU cc_start: 0.8693 (tp30) cc_final: 0.8121 (tp30) REVERT: i 62 TYR cc_start: 0.8733 (t80) cc_final: 0.8275 (t80) REVERT: i 113 LYS cc_start: 0.9359 (mptt) cc_final: 0.8964 (mmtm) REVERT: j 45 ARG cc_start: 0.8252 (ttt180) cc_final: 0.7801 (tpt-90) REVERT: j 47 GLU cc_start: 0.8730 (tt0) cc_final: 0.8371 (tt0) REVERT: j 64 GLN cc_start: 0.9038 (mp10) cc_final: 0.8714 (mp10) REVERT: j 78 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8843 (pp30) REVERT: l 29 GLN cc_start: 0.6937 (mp10) cc_final: 0.5821 (pm20) REVERT: l 57 LEU cc_start: 0.7955 (tp) cc_final: 0.7701 (tp) REVERT: l 75 GLN cc_start: 0.8521 (mm110) cc_final: 0.8262 (pm20) REVERT: m 50 ASP cc_start: 0.8451 (t70) cc_final: 0.8062 (t0) REVERT: m 81 MET cc_start: 0.8927 (mtt) cc_final: 0.8386 (mtt) REVERT: n 26 GLU cc_start: 0.9164 (pt0) cc_final: 0.8960 (pp20) REVERT: n 92 ASP cc_start: 0.8347 (m-30) cc_final: 0.8068 (m-30) REVERT: o 51 HIS cc_start: 0.8879 (m90) cc_final: 0.8571 (m90) REVERT: q 4 LYS cc_start: 0.4222 (mmtt) cc_final: 0.2967 (mmmt) REVERT: q 25 LEU cc_start: 0.9244 (tp) cc_final: 0.8998 (tp) REVERT: q 34 LEU cc_start: 0.9518 (tp) cc_final: 0.9220 (tt) REVERT: r 21 ILE cc_start: 0.5217 (mm) cc_final: 0.4760 (mt) outliers start: 6 outliers final: 2 residues processed: 351 average time/residue: 0.6521 time to fit residues: 372.6030 Evaluate side-chains 274 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 271 time to evaluate : 2.938 ------------------------------------------------------------------------------- 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: 1.9990 chunk 257 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 343 optimal weight: 0.5980 chunk 363 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 325 optimal weight: 0.0270 chunk 97 optimal weight: 9.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 111 GLN c 28 GLN c 139 GLN c 213 GLN d 73 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN e 134 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS g 21 GLN h 98 GLN ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** 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** m 52 GLN ** q 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 55029 Z= 0.146 Angle : 0.616 12.458 81889 Z= 0.331 Chirality : 0.034 0.476 10392 Planarity : 0.006 0.121 4722 Dihedral : 23.988 179.916 26382 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.04 % 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: -0.49 (0.17), residues: 2273 helix: 0.12 (0.17), residues: 872 sheet: 0.22 (0.27), residues: 367 loop : -0.82 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP g 103 HIS 0.004 0.001 HIS f 3 PHE 0.014 0.001 PHE d 109 TYR 0.015 0.001 TYR l 95 ARG 0.007 0.001 ARG b 110 *********************** 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 371 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 369 time to evaluate : 3.013 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: b 111 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6389 (pp30) REVERT: c 123 GLN cc_start: 0.9290 (mm110) cc_final: 0.8873 (mm-40) REVERT: e 96 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7230 (pp30) REVERT: f 54 ILE cc_start: 0.8561 (pt) cc_final: 0.8246 (tp) REVERT: h 93 LEU cc_start: 0.8950 (mt) cc_final: 0.8481 (mt) REVERT: i 54 GLU cc_start: 0.9127 (pm20) cc_final: 0.8817 (pm20) REVERT: i 62 TYR cc_start: 0.8717 (t80) cc_final: 0.8174 (t80) REVERT: j 47 GLU cc_start: 0.8750 (tt0) cc_final: 0.8412 (tt0) REVERT: j 49 PHE cc_start: 0.8779 (m-80) cc_final: 0.8081 (m-80) REVERT: j 53 THR cc_start: 0.8542 (p) cc_final: 0.8337 (p) REVERT: j 66 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6845 (tm-30) REVERT: j 78 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8753 (pp30) REVERT: l 21 VAL cc_start: 0.8117 (m) cc_final: 0.7861 (m) REVERT: l 29 GLN cc_start: 0.6582 (mp10) cc_final: 0.5479 (pm20) REVERT: l 57 LEU cc_start: 0.8063 (tp) cc_final: 0.7845 (tp) REVERT: l 75 GLN cc_start: 0.8487 (mm110) cc_final: 0.8226 (pm20) REVERT: l 88 LYS cc_start: 0.8305 (ttpt) cc_final: 0.7778 (mttm) REVERT: m 31 LYS cc_start: 0.9125 (pttp) cc_final: 0.8818 (pttm) REVERT: m 50 ASP cc_start: 0.8247 (t70) cc_final: 0.7928 (t0) REVERT: m 81 MET cc_start: 0.8654 (mtt) cc_final: 0.8185 (mtt) REVERT: n 40 GLU cc_start: 0.9307 (pt0) cc_final: 0.9062 (pt0) REVERT: n 45 MET cc_start: 0.9439 (mmm) cc_final: 0.9123 (mmp) REVERT: n 48 LEU cc_start: 0.9501 (pp) cc_final: 0.9212 (pp) REVERT: n 88 VAL cc_start: 0.9275 (p) cc_final: 0.8930 (p) REVERT: n 90 GLN cc_start: 0.9342 (pm20) cc_final: 0.9104 (pm20) REVERT: n 92 ASP cc_start: 0.8641 (m-30) cc_final: 0.8252 (m-30) REVERT: o 51 HIS cc_start: 0.8671 (m90) cc_final: 0.8340 (m90) REVERT: q 4 LYS cc_start: 0.4104 (mmtt) cc_final: 0.2888 (mmmt) REVERT: q 25 LEU cc_start: 0.9380 (tp) cc_final: 0.8960 (tp) REVERT: q 34 LEU cc_start: 0.9542 (tp) cc_final: 0.9203 (tt) REVERT: r 32 TYR cc_start: 0.7689 (m-80) cc_final: 0.6918 (m-10) REVERT: r 40 VAL cc_start: 0.7034 (m) cc_final: 0.6738 (m) REVERT: s 16 PHE cc_start: 0.9383 (t80) cc_final: 0.8636 (t80) REVERT: s 41 LEU cc_start: 0.9520 (mm) cc_final: 0.9250 (mm) REVERT: s 64 GLU cc_start: 0.8319 (pm20) cc_final: 0.7700 (pm20) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.6431 time to fit residues: 392.9244 Evaluate side-chains 290 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 288 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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: 20.0000 chunk 206 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 270 optimal weight: 0.2980 chunk 149 optimal weight: 20.0000 chunk 310 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 326 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- 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 ** d 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 52 GLN r 54 GLN r 61 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 55029 Z= 0.346 Angle : 0.777 12.334 81889 Z= 0.404 Chirality : 0.040 0.534 10392 Planarity : 0.007 0.124 4722 Dihedral : 24.262 179.757 26382 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 31.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: -0.88 (0.17), residues: 2273 helix: -0.16 (0.17), residues: 863 sheet: -0.21 (0.26), residues: 369 loop : -0.98 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP b 98 HIS 0.018 0.002 HIS b 170 PHE 0.022 0.003 PHE h 67 TYR 0.020 0.002 TYR d 78 ARG 0.013 0.001 ARG g 79 *********************** 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 336 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 3.351 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: c 110 ASP cc_start: 0.8374 (m-30) cc_final: 0.7363 (t70) REVERT: c 123 GLN cc_start: 0.9273 (mm110) cc_final: 0.8962 (mp10) REVERT: d 94 LYS cc_start: 0.9650 (mtpt) cc_final: 0.9344 (mmmt) REVERT: e 158 LYS cc_start: 0.8579 (mmtp) cc_final: 0.8108 (mptt) REVERT: f 54 ILE cc_start: 0.8562 (pt) cc_final: 0.8324 (tp) REVERT: g 89 MET cc_start: 0.6252 (tpt) cc_final: 0.5823 (ttt) REVERT: h 60 LEU cc_start: 0.9386 (tp) cc_final: 0.9157 (tp) REVERT: h 93 LEU cc_start: 0.9034 (mt) cc_final: 0.8565 (mt) REVERT: i 62 TYR cc_start: 0.8704 (t80) cc_final: 0.8224 (t80) REVERT: i 113 LYS cc_start: 0.9280 (mptt) cc_final: 0.8976 (mmtm) REVERT: j 45 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7601 (tpt-90) REVERT: j 47 GLU cc_start: 0.8799 (tt0) cc_final: 0.8389 (tt0) REVERT: j 66 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6520 (tm-30) REVERT: j 78 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8812 (pp30) REVERT: k 84 LEU cc_start: 0.6788 (mm) cc_final: 0.6580 (mp) REVERT: l 29 GLN cc_start: 0.6769 (mp10) cc_final: 0.6198 (mp10) REVERT: l 57 LEU cc_start: 0.8126 (tp) cc_final: 0.7886 (tp) REVERT: l 75 GLN cc_start: 0.8544 (mm110) cc_final: 0.8293 (pm20) REVERT: l 88 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7628 (mttm) REVERT: m 31 LYS cc_start: 0.9105 (pttp) cc_final: 0.8726 (pttm) REVERT: m 50 ASP cc_start: 0.8119 (t70) cc_final: 0.7712 (t0) REVERT: m 54 ASP cc_start: 0.8095 (p0) cc_final: 0.7849 (p0) REVERT: m 81 MET cc_start: 0.8775 (mtt) cc_final: 0.8305 (mtt) REVERT: n 40 GLU cc_start: 0.9440 (pt0) cc_final: 0.9234 (pt0) REVERT: n 45 MET cc_start: 0.9457 (mmm) cc_final: 0.9170 (mmp) REVERT: n 48 LEU cc_start: 0.9524 (pp) cc_final: 0.9253 (pp) REVERT: n 92 ASP cc_start: 0.8630 (m-30) cc_final: 0.8251 (m-30) REVERT: o 51 HIS cc_start: 0.8801 (m90) cc_final: 0.8504 (m90) REVERT: q 4 LYS cc_start: 0.4050 (mmtt) cc_final: 0.2858 (mmmt) REVERT: r 21 ILE cc_start: 0.2641 (mm) cc_final: 0.1952 (mt) REVERT: s 41 LEU cc_start: 0.9437 (mm) cc_final: 0.9140 (mm) REVERT: s 44 PHE cc_start: 0.9361 (m-80) cc_final: 0.9113 (m-80) REVERT: s 64 GLU cc_start: 0.8415 (pm20) cc_final: 0.7997 (pm20) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.6558 time to fit residues: 362.5374 Evaluate side-chains 272 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 3.005 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 363 optimal weight: 0.9980 chunk 301 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 ASN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 HIS ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 28 GLN g 21 GLN ** j 56 HIS ** 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 52 GLN ** n 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 55029 Z= 0.345 Angle : 0.814 12.109 81889 Z= 0.423 Chirality : 0.042 0.573 10392 Planarity : 0.007 0.125 4722 Dihedral : 24.577 179.880 26382 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 34.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.46 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -1.30 (0.17), residues: 2273 helix: -0.54 (0.16), residues: 857 sheet: -0.43 (0.27), residues: 342 loop : -1.19 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP b 98 HIS 0.017 0.002 HIS b 170 PHE 0.027 0.003 PHE b 24 TYR 0.031 0.003 TYR r 51 ARG 0.021 0.001 ARG b 97 *********************** 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 324 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.967 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: b 24 PHE cc_start: 0.8406 (m-10) cc_final: 0.8160 (m-80) REVERT: b 66 LYS cc_start: 0.8624 (pptt) cc_final: 0.8072 (tppt) REVERT: b 170 HIS cc_start: 0.4850 (t70) cc_final: 0.4635 (t-90) REVERT: c 43 LEU cc_start: 0.9115 (mt) cc_final: 0.8631 (mt) REVERT: c 110 ASP cc_start: 0.8549 (m-30) cc_final: 0.6896 (t0) REVERT: c 123 GLN cc_start: 0.9217 (mm110) cc_final: 0.8939 (mp10) REVERT: d 4 TYR cc_start: 0.7994 (t80) cc_final: 0.7789 (t80) REVERT: d 74 PHE cc_start: 0.8885 (t80) cc_final: 0.8488 (t80) REVERT: d 94 LYS cc_start: 0.9668 (mtpt) cc_final: 0.9350 (mmmm) REVERT: e 70 MET cc_start: 0.7524 (mmp) cc_final: 0.7115 (tmm) REVERT: e 96 GLN cc_start: 0.7859 (pp30) cc_final: 0.7489 (pp30) REVERT: f 54 ILE cc_start: 0.8740 (pt) cc_final: 0.8392 (tp) REVERT: g 27 MET cc_start: 0.8586 (mtt) cc_final: 0.8023 (mmp) REVERT: h 60 LEU cc_start: 0.9318 (tp) cc_final: 0.9111 (tp) REVERT: h 65 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7435 (mtpp) REVERT: h 93 LEU cc_start: 0.9175 (mt) cc_final: 0.8663 (mt) REVERT: i 62 TYR cc_start: 0.8666 (t80) cc_final: 0.8196 (t80) REVERT: i 113 LYS cc_start: 0.9399 (mptt) cc_final: 0.8742 (mptt) REVERT: j 45 ARG cc_start: 0.8316 (ttt180) cc_final: 0.8113 (ttm-80) REVERT: j 47 GLU cc_start: 0.8840 (tt0) cc_final: 0.8428 (tt0) REVERT: j 66 GLU cc_start: 0.7824 (tm-30) cc_final: 0.6582 (tm-30) REVERT: j 78 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8812 (pp30) REVERT: l 57 LEU cc_start: 0.8078 (tp) cc_final: 0.7823 (tp) REVERT: l 62 GLU cc_start: 0.8013 (pm20) cc_final: 0.7806 (pm20) REVERT: l 75 GLN cc_start: 0.8710 (mm110) cc_final: 0.8379 (pm20) REVERT: l 88 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7166 (mttp) REVERT: m 49 ASP cc_start: 0.8643 (m-30) cc_final: 0.8324 (m-30) REVERT: m 50 ASP cc_start: 0.8117 (t70) cc_final: 0.7610 (t0) REVERT: m 54 ASP cc_start: 0.8169 (p0) cc_final: 0.7880 (p0) REVERT: m 81 MET cc_start: 0.8703 (mtt) cc_final: 0.8283 (mtt) REVERT: n 45 MET cc_start: 0.9450 (mmm) cc_final: 0.9171 (mmp) REVERT: n 48 LEU cc_start: 0.9535 (pp) cc_final: 0.9269 (pp) REVERT: n 92 ASP cc_start: 0.8807 (m-30) cc_final: 0.8502 (m-30) REVERT: n 101 TRP cc_start: 0.8508 (p90) cc_final: 0.8249 (p90) REVERT: o 51 HIS cc_start: 0.8888 (m90) cc_final: 0.8588 (m90) REVERT: q 4 LYS cc_start: 0.3790 (mmtt) cc_final: 0.2639 (mmmt) REVERT: q 25 LEU cc_start: 0.9176 (tp) cc_final: 0.8940 (tp) REVERT: q 31 GLN cc_start: 0.8272 (mp10) cc_final: 0.7867 (mm-40) REVERT: r 25 ASP cc_start: 0.7102 (p0) cc_final: 0.6708 (p0) REVERT: r 63 ARG cc_start: 0.5697 (ttm170) cc_final: 0.5133 (ttm170) REVERT: s 20 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8764 (mt-10) REVERT: s 41 LEU cc_start: 0.9458 (mm) cc_final: 0.9177 (mm) REVERT: s 44 PHE cc_start: 0.9487 (m-80) cc_final: 0.9177 (m-80) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.6752 time to fit residues: 357.7415 Evaluate side-chains 268 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.987 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 362 optimal weight: 0.6980 chunk 226 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 d 102 ASN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** j 56 HIS ** 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 52 GLN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 GLN ** r 54 GLN ** 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: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55029 Z= 0.189 Angle : 0.657 12.296 81889 Z= 0.348 Chirality : 0.036 0.521 10392 Planarity : 0.006 0.123 4722 Dihedral : 24.302 179.316 26382 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.11 % Allowed : 1.53 % Favored : 98.36 % 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: -0.81 (0.17), residues: 2273 helix: 0.08 (0.17), residues: 862 sheet: -0.37 (0.27), residues: 353 loop : -1.03 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP g 103 HIS 0.021 0.001 HIS b 96 PHE 0.020 0.002 PHE g 61 TYR 0.021 0.002 TYR c 168 ARG 0.009 0.001 ARG o 88 *********************** 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 357 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 355 time to evaluate : 3.228 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: b 24 PHE cc_start: 0.8509 (m-10) cc_final: 0.8245 (m-80) REVERT: b 143 MET cc_start: 0.7417 (mmm) cc_final: 0.6941 (mmp) REVERT: b 156 MET cc_start: 0.3385 (tmm) cc_final: 0.0524 (mmm) REVERT: c 110 ASP cc_start: 0.8511 (m-30) cc_final: 0.8303 (p0) REVERT: c 123 GLN cc_start: 0.9229 (mm110) cc_final: 0.8890 (mm-40) REVERT: d 74 PHE cc_start: 0.8749 (t80) cc_final: 0.8426 (t80) REVERT: d 94 LYS cc_start: 0.9647 (mtpt) cc_final: 0.9377 (mmmt) REVERT: e 96 GLN cc_start: 0.7771 (pp30) cc_final: 0.7472 (pp30) REVERT: e 158 LYS cc_start: 0.8553 (mmtp) cc_final: 0.7999 (mptt) REVERT: f 54 ILE cc_start: 0.8705 (pt) cc_final: 0.8377 (tp) REVERT: g 101 MET cc_start: 0.7074 (ttp) cc_final: 0.6196 (tmm) REVERT: h 65 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7411 (mttt) REVERT: h 93 LEU cc_start: 0.9048 (mt) cc_final: 0.8528 (mt) REVERT: i 62 TYR cc_start: 0.8621 (t80) cc_final: 0.8133 (t80) REVERT: i 113 LYS cc_start: 0.9329 (mptt) cc_final: 0.8725 (mptt) REVERT: j 47 GLU cc_start: 0.8803 (tt0) cc_final: 0.8427 (tt0) REVERT: j 49 PHE cc_start: 0.8819 (m-80) cc_final: 0.8143 (m-80) REVERT: j 66 GLU cc_start: 0.7294 (tm-30) cc_final: 0.7009 (tm-30) REVERT: j 78 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8792 (pp30) REVERT: l 21 VAL cc_start: 0.8270 (m) cc_final: 0.8065 (m) REVERT: l 57 LEU cc_start: 0.8029 (tp) cc_final: 0.7773 (tp) REVERT: l 75 GLN cc_start: 0.8582 (mm110) cc_final: 0.8251 (pm20) REVERT: l 88 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7282 (mttp) REVERT: l 97 THR cc_start: 0.9353 (m) cc_final: 0.9038 (p) REVERT: m 50 ASP cc_start: 0.7674 (t70) cc_final: 0.7282 (t0) REVERT: m 54 ASP cc_start: 0.8045 (p0) cc_final: 0.7771 (p0) REVERT: m 81 MET cc_start: 0.8551 (mtt) cc_final: 0.8186 (mtt) REVERT: n 45 MET cc_start: 0.9375 (mmm) cc_final: 0.9082 (mmp) REVERT: n 48 LEU cc_start: 0.9526 (pp) cc_final: 0.9166 (pp) REVERT: n 92 ASP cc_start: 0.8654 (m-30) cc_final: 0.8424 (m-30) REVERT: o 51 HIS cc_start: 0.8779 (m90) cc_final: 0.8472 (m90) REVERT: q 4 LYS cc_start: 0.3831 (mmtt) cc_final: 0.2722 (mmmt) REVERT: q 25 LEU cc_start: 0.9101 (tp) cc_final: 0.8875 (tp) REVERT: q 31 GLN cc_start: 0.8081 (mp-120) cc_final: 0.7727 (mm-40) REVERT: r 25 ASP cc_start: 0.7095 (p0) cc_final: 0.6665 (p0) REVERT: r 63 ARG cc_start: 0.5762 (ttm170) cc_final: 0.5333 (ttm170) REVERT: r 64 TYR cc_start: 0.8242 (t80) cc_final: 0.7990 (t80) REVERT: s 41 LEU cc_start: 0.9458 (mm) cc_final: 0.9209 (mm) REVERT: s 44 PHE cc_start: 0.9476 (m-80) cc_final: 0.9137 (m-80) outliers start: 2 outliers final: 0 residues processed: 356 average time/residue: 0.6407 time to fit residues: 374.6183 Evaluate side-chains 288 residues out of total 1891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.4558 > 50: distance: 39 - 187: 29.492 distance: 42 - 184: 16.776 distance: 58 - 171: 14.801 distance: 61 - 168: 28.863 distance: 72 - 152: 23.475 distance: 75 - 149: 29.340 distance: 121 - 163: 25.879 distance: 124 - 160: 21.685 distance: 144 - 149: 28.727 distance: 149 - 150: 48.447 distance: 150 - 151: 32.049 distance: 150 - 153: 39.070 distance: 151 - 152: 44.931 distance: 151 - 160: 18.673 distance: 153 - 154: 37.388 distance: 154 - 155: 36.317 distance: 155 - 156: 17.433 distance: 156 - 157: 13.039 distance: 157 - 158: 14.804 distance: 157 - 159: 21.122 distance: 160 - 161: 48.903 distance: 161 - 162: 24.061 distance: 161 - 164: 52.346 distance: 162 - 163: 31.532 distance: 162 - 168: 39.157 distance: 164 - 165: 18.737 distance: 165 - 166: 16.995 distance: 165 - 167: 21.765 distance: 168 - 169: 4.296 distance: 169 - 170: 48.996 distance: 169 - 172: 38.642 distance: 170 - 171: 34.605 distance: 170 - 176: 12.303 distance: 172 - 173: 21.969 distance: 172 - 174: 32.952 distance: 173 - 175: 23.043 distance: 176 - 177: 30.244 distance: 177 - 178: 7.957 distance: 177 - 180: 14.497 distance: 178 - 179: 21.188 distance: 178 - 184: 22.196 distance: 180 - 181: 29.633 distance: 181 - 182: 31.444 distance: 181 - 183: 15.481 distance: 184 - 185: 8.883 distance: 185 - 186: 26.769 distance: 185 - 188: 47.676 distance: 186 - 187: 21.084 distance: 186 - 192: 46.051 distance: 188 - 189: 11.605 distance: 188 - 190: 20.860 distance: 189 - 191: 12.234 distance: 192 - 193: 38.663 distance: 193 - 194: 34.364 distance: 193 - 196: 27.093 distance: 194 - 195: 49.531 distance: 194 - 199: 10.467 distance: 196 - 197: 31.515 distance: 196 - 198: 33.212 distance: 199 - 200: 52.032 distance: 200 - 201: 34.722 distance: 200 - 203: 35.107 distance: 201 - 202: 12.746 distance: 201 - 208: 13.040 distance: 203 - 204: 18.025 distance: 204 - 205: 49.649 distance: 205 - 206: 5.784 distance: 205 - 207: 20.973 distance: 208 - 209: 10.693 distance: 208 - 214: 10.827 distance: 209 - 210: 25.037 distance: 209 - 212: 44.292 distance: 210 - 211: 43.419 distance: 210 - 215: 30.110 distance: 212 - 213: 18.475 distance: 213 - 214: 48.141 distance: 215 - 216: 32.520 distance: 216 - 217: 15.857 distance: 216 - 219: 49.682 distance: 217 - 218: 37.937 distance: 217 - 222: 39.928 distance: 219 - 220: 28.813 distance: 219 - 221: 31.811 distance: 222 - 223: 13.164 distance: 223 - 224: 25.046 distance: 223 - 226: 49.098 distance: 224 - 225: 36.771 distance: 224 - 230: 18.269 distance: 226 - 227: 40.732 distance: 227 - 228: 10.671 distance: 227 - 229: 5.806