Starting phenix.real_space_refine on Mon Nov 20 13:41:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap4_15558/11_2023/8ap4_15558_updated.pdb" } resolution = 3.0 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= 0.011 sd= 0.085 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 2940 5.49 5 S 81 5.16 5 C 44136 2.51 5 N 16545 2.21 5 O 24912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 72": "OD1" <-> "OD2" Residue "c TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "d PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d ASP 18": "OD1" <-> "OD2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "e GLU 16": "OE1" <-> "OE2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "e GLU 144": "OE1" <-> "OE2" Residue "e ASP 145": "OD1" <-> "OD2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e GLU 198": "OE1" <-> "OE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 46": "OD1" <-> "OD2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 142": "OD1" <-> "OD2" Residue "f ASP 144": "OD1" <-> "OD2" Residue "f ASP 163": "OD1" <-> "OD2" Residue "f ASP 174": "OD1" <-> "OD2" Residue "g ASP 39": "OD1" <-> "OD2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "h TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 14": "OD1" <-> "OD2" Residue "i TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i ASP 71": "OD1" <-> "OD2" Residue "i TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 37": "OD1" <-> "OD2" Residue "j ASP 80": "OD1" <-> "OD2" Residue "j GLU 110": "OE1" <-> "OE2" Residue "k GLU 86": "OE1" <-> "OE2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "l PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 112": "OE1" <-> "OE2" Residue "o ASP 16": "OD1" <-> "OD2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o GLU 34": "OE1" <-> "OE2" Residue "o PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "p GLU 89": "OE1" <-> "OE2" Residue "p ASP 97": "OD1" <-> "OD2" Residue "q PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 67": "OD1" <-> "OD2" Residue "s TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 89": "OD1" <-> "OD2" Residue "u ASP 43": "OD1" <-> "OD2" Residue "u GLU 55": "OE1" <-> "OE2" Residue "u TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 56": "OD1" <-> "OD2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "x GLU 5": "OE1" <-> "OE2" Residue "y GLU 39": "OE1" <-> "OE2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ASP 46": "OD1" <-> "OD2" Residue "z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 88614 Number of models: 1 Model: "" Number of chains: 33 Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "A" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 820 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "Z" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1521 Classifications: {'RNA': 71} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 59} Chain breaks: 1 Chain: "a" Number of atoms: 59067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2750, 59067 Classifications: {'RNA': 2750} Modifications used: {'rna2p': 6, 'rna2p_pur': 268, 'rna2p_pyr': 140, 'rna3p': 16, 'rna3p_pur': 1316, 'rna3p_pyr': 1004} Link IDs: {'rna2p': 413, 'rna3p': 2336} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 592 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Time building chain proxies: 35.14, per 1000 atoms: 0.40 Number of scatterers: 88614 At special positions: 0 Unit cell: (228.228, 191.444, 216.524, 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 81 16.00 P 2940 15.00 O 24912 8.00 N 16545 7.00 C 44136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 4 18 " - pdb=" SG CYS 4 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 37 " - pdb=" SG CYS 4 40 " 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=0, symmetry=0 Time building additional restraints: 42.04 Conformation dependent library (CDL) restraints added in 4.6 seconds 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5962 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 48 sheets defined 26.5% alpha, 19.3% beta 1022 base pairs and 1534 stacking pairs defined. Time for finding SS restraints: 45.32 Creating SS restraints... Processing helix chain '1' and resid 9 through 16 Processing helix chain '1' and resid 18 through 23 Processing helix chain '1' and resid 25 through 37 Processing helix chain '2' and resid 8 through 11 No H-bonds generated for 'chain '2' and resid 8 through 11' Processing helix chain '2' and resid 38 through 45 Processing helix chain '2' and resid 52 through 61 removed outlier: 4.245A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 33 No H-bonds generated for 'chain '3' and resid 31 through 33' Processing helix chain '4' and resid 42 through 45 No H-bonds generated for 'chain '4' and resid 42 through 45' Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 78 through 84 removed outlier: 4.046A pdb=" N LEU A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 Processing helix chain 'c' and resid 11 through 14 No H-bonds generated for 'chain 'c' and resid 11 through 14' Processing helix chain 'c' and resid 31 through 33 No H-bonds generated for 'chain 'c' and resid 31 through 33' Processing helix chain 'c' and resid 198 through 202 removed outlier: 3.577A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 213 Processing helix chain 'c' and resid 264 through 266 No H-bonds generated for 'chain 'c' and resid 264 through 266' Processing helix chain 'd' and resid 40 through 43 No H-bonds generated for 'chain 'd' and resid 40 through 43' Processing helix chain 'd' and resid 62 through 71 removed outlier: 3.702A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 99 through 101 No H-bonds generated for 'chain 'd' and resid 99 through 101' Processing helix chain 'd' and resid 121 through 125 Processing helix chain 'e' and resid 16 through 20 Processing helix chain 'e' and resid 25 through 39 Processing helix chain 'e' and resid 98 through 114 Processing helix chain 'e' and resid 131 through 141 Processing helix chain 'e' and resid 155 through 163 removed outlier: 4.007A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 174 No H-bonds generated for 'chain 'e' and resid 172 through 174' Processing helix chain 'e' and resid 177 through 182 Processing helix chain 'e' and resid 190 through 199 Processing helix chain 'f' and resid 3 through 20 removed outlier: 3.900A pdb=" N VAL f 12 " --> pdb=" O TYR f 8 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 27 No H-bonds generated for 'chain 'f' and resid 25 through 27' Processing helix chain 'f' and resid 41 through 44 removed outlier: 3.573A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 41 through 44' Processing helix chain 'f' and resid 48 through 61 Processing helix chain 'f' and resid 93 through 110 removed outlier: 3.618A pdb=" N PHE f 99 " --> pdb=" O MET f 96 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ALA f 107 " --> pdb=" O ILE f 104 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL f 108 " --> pdb=" O THR f 105 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 163 through 172 Processing helix chain 'g' and resid 3 through 6 No H-bonds generated for 'chain 'g' and resid 3 through 6' Processing helix chain 'g' and resid 62 through 80 Processing helix chain 'g' and resid 138 through 152 removed outlier: 4.345A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 29 Processing helix chain 'i' and resid 25 through 37 Processing helix chain 'i' and resid 59 through 61 No H-bonds generated for 'chain 'i' and resid 59 through 61' Processing helix chain 'i' and resid 66 through 71 removed outlier: 4.234A pdb=" N ARG i 69 " --> pdb=" O GLY i 66 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP i 71 " --> pdb=" O LYS i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 89 through 95 Processing helix chain 'i' and resid 97 through 108 removed outlier: 4.643A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 121 removed outlier: 3.931A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 113 through 118 Processing helix chain 'k' and resid 37 through 40 No H-bonds generated for 'chain 'k' and resid 37 through 40' Processing helix chain 'k' and resid 57 through 60 No H-bonds generated for 'chain 'k' and resid 57 through 60' Processing helix chain 'k' and resid 69 through 72 Processing helix chain 'k' and resid 79 through 82 No H-bonds generated for 'chain 'k' and resid 79 through 82' Processing helix chain 'k' and resid 92 through 98 Processing helix chain 'k' and resid 129 through 138 Processing helix chain 'l' and resid 43 through 57 Processing helix chain 'l' and resid 110 through 123 removed outlier: 3.594A pdb=" N ALA l 122 " --> pdb=" O LYS l 118 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 31 Processing helix chain 'm' and resid 38 through 55 removed outlier: 4.093A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix Processing helix chain 'm' and resid 60 through 68 Processing helix chain 'm' and resid 73 through 81 Processing helix chain 'm' and resid 83 through 86 No H-bonds generated for 'chain 'm' and resid 83 through 86' Processing helix chain 'n' and resid 3 through 21 removed outlier: 4.424A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.861A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 68 through 85 Processing helix chain 'n' and resid 102 through 112 Processing helix chain 'o' and resid 3 through 10 Processing helix chain 'o' and resid 54 through 56 No H-bonds generated for 'chain 'o' and resid 54 through 56' Processing helix chain 'o' and resid 98 through 102 Processing helix chain 'p' and resid 7 through 21 Processing helix chain 'p' and resid 26 through 29 Processing helix chain 'p' and resid 32 through 72 removed outlier: 3.826A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 85 Processing helix chain 'p' and resid 92 through 101 Processing helix chain 'p' and resid 103 through 117 Processing helix chain 'r' and resid 14 through 24 removed outlier: 3.687A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 38 removed outlier: 3.714A pdb=" N TYR r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 61 Processing helix chain 'r' and resid 89 through 91 No H-bonds generated for 'chain 'r' and resid 89 through 91' Processing helix chain 's' and resid 4 through 10 Processing helix chain 's' and resid 18 through 26 Processing helix chain 's' and resid 40 through 51 Processing helix chain 't' and resid 67 through 69 No H-bonds generated for 'chain 't' and resid 67 through 69' Processing helix chain 'u' and resid 14 through 22 Processing helix chain 'u' and resid 44 through 52 removed outlier: 3.572A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 58 Processing helix chain 'w' and resid 53 through 62 Processing helix chain 'w' and resid 64 through 74 Processing helix chain 'x' and resid 3 through 7 Processing helix chain 'x' and resid 11 through 34 Processing helix chain 'x' and resid 41 through 60 removed outlier: 3.569A pdb=" N ARG x 47 " --> pdb=" O LEU x 43 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 27 Processing helix chain 'y' and resid 42 through 50 Processing helix chain 'z' and resid 10 through 20 removed outlier: 4.739A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP z 20 " --> pdb=" O ARG z 16 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 20 through 25 Processing sheet with id= B, first strand: chain '3' and resid 2 through 4 Processing sheet with id= C, first strand: chain '3' and resid 15 through 19 Processing sheet with id= D, first strand: chain '4' and resid 21 through 26 removed outlier: 3.893A pdb=" N MET 4 22 " --> pdb=" O ALA 4 14 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA 4 14 " --> pdb=" O MET 4 22 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU 4 32 " --> pdb=" O SER 4 15 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 55 through 59 removed outlier: 3.734A pdb=" N VAL A 66 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 3 through 5 Processing sheet with id= G, first strand: chain 'c' and resid 34 through 36 Processing sheet with id= H, first strand: chain 'c' and resid 101 through 105 removed outlier: 3.834A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'c' and resid 129 through 131 Processing sheet with id= J, first strand: chain 'c' and resid 181 through 185 removed outlier: 3.691A pdb=" N ALA c 166 " --> pdb=" O THR c 173 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'd' and resid 169 through 172 removed outlier: 4.668A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG d 179 " --> pdb=" O LEU d 188 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS d 190 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL d 177 " --> pdb=" O LYS d 190 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'd' and resid 78 through 83 removed outlier: 4.495A pdb=" N GLY d 78 " --> pdb=" O THR d 52 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR d 52 " --> pdb=" O GLY d 78 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'e' and resid 2 through 4 Processing sheet with id= N, first strand: chain 'e' and resid 118 through 120 removed outlier: 6.261A pdb=" N VAL e 186 " --> pdb=" O ILE e 119 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'f' and resid 66 through 68 removed outlier: 4.351A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS f 87 " --> pdb=" O MET f 38 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR f 157 " --> pdb=" O GLU f 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE f 34 " --> pdb=" O THR f 155 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR f 155 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU f 36 " --> pdb=" O ASP f 153 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP f 153 " --> pdb=" O LEU f 36 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'g' and resid 16 through 20 Processing sheet with id= Q, first strand: chain 'g' and resid 42 through 46 Processing sheet with id= R, first strand: chain 'g' and resid 161 through 164 removed outlier: 3.585A pdb=" N GLY g 161 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'g' and resid 95 through 99 removed outlier: 3.614A pdb=" N ARG g 95 " --> pdb=" O SER g 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER g 106 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL g 113 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'h' and resid 18 through 20 Processing sheet with id= U, first strand: chain 'i' and resid 15 through 19 removed outlier: 6.477A pdb=" N TYR i 53 " --> pdb=" O TYR i 16 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL i 18 " --> pdb=" O TYR i 53 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE i 55 " --> pdb=" O VAL i 18 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'i' and resid 73 through 77 Processing sheet with id= W, first strand: chain 'j' and resid 6 through 9 removed outlier: 3.939A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL j 24 " --> pdb=" O ILE j 38 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ILE j 38 " --> pdb=" O VAL j 24 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA j 83 " --> pdb=" O VAL j 63 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'k' and resid 74 through 78 removed outlier: 6.818A pdb=" N PHE k 107 " --> pdb=" O ALA k 75 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE k 77 " --> pdb=" O PHE k 107 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS k 109 " --> pdb=" O ILE k 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'k' and resid 121 through 123 removed outlier: 7.110A pdb=" N LYS k 141 " --> pdb=" O VAL k 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'l' and resid 128 through 132 removed outlier: 3.524A pdb=" N THR l 129 " --> pdb=" O LYS l 34 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'l' and resid 39 through 42 removed outlier: 7.157A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP l 92 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS l 71 " --> pdb=" O TRP l 92 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'm' and resid 33 through 37 removed outlier: 3.837A pdb=" N GLY m 101 " --> pdb=" O MET m 110 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N TYR m 112 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS m 99 " --> pdb=" O TYR m 112 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLU m 114 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE m 97 " --> pdb=" O GLU m 114 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'n' and resid 91 through 93 removed outlier: 4.122A pdb=" N VAL n 28 " --> pdb=" O ASP n 93 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'o' and resid 81 through 86 removed outlier: 6.545A pdb=" N LYS o 29 " --> pdb=" O ASP o 82 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE o 84 " --> pdb=" O GLU o 27 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU o 27 " --> pdb=" O ILE o 84 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL o 86 " --> pdb=" O THR o 25 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR o 25 " --> pdb=" O VAL o 86 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY o 45 " --> pdb=" O VAL o 26 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLU o 44 " --> pdb=" O ILE o 64 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE o 64 " --> pdb=" O GLU o 44 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE o 48 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE o 50 " --> pdb=" O ALA o 58 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA o 58 " --> pdb=" O ILE o 50 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'q' and resid 10 through 15 removed outlier: 3.745A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLN q 6 " --> pdb=" O VAL q 38 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL q 38 " --> pdb=" O GLN q 6 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE q 41 " --> pdb=" O LYS q 48 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'q' and resid 19 through 22 removed outlier: 3.766A pdb=" N ALA q 65 " --> pdb=" O ASP q 95 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'q' and resid 32 through 35 removed outlier: 6.363A pdb=" N GLU q 62 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE q 98 " --> pdb=" O GLU q 62 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'q' and resid 72 through 78 removed outlier: 3.558A pdb=" N HIS q 89 " --> pdb=" O VAL q 72 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'r' and resid 3 through 7 removed outlier: 4.464A pdb=" N THR r 100 " --> pdb=" O GLY r 79 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER r 108 " --> pdb=" O VAL r 71 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL r 71 " --> pdb=" O SER r 108 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'r' and resid 82 through 87 Processing sheet with id= AK, first strand: chain 's' and resid 11 through 14 removed outlier: 6.869A pdb=" N LYS s 33 " --> pdb=" O ARG s 12 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL s 31 " --> pdb=" O PRO s 14 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL s 57 " --> pdb=" O THR s 86 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 's' and resid 67 through 70 Processing sheet with id= AM, first strand: chain 't' and resid 22 through 24 Processing sheet with id= AN, first strand: chain 't' and resid 42 through 45 Processing sheet with id= AO, first strand: chain 't' and resid 83 through 88 Processing sheet with id= AP, first strand: chain 't' and resid 25 through 28 removed outlier: 6.957A pdb=" N ILE t 35 " --> pdb=" O LYS t 26 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'u' and resid 62 through 65 removed outlier: 7.885A pdb=" N ASN u 5 " --> pdb=" O ASP u 43 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP u 43 " --> pdb=" O ASN u 5 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE u 89 " --> pdb=" O ILE u 29 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TYR u 31 " --> pdb=" O ILE u 89 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE u 91 " --> pdb=" O TYR u 31 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP u 76 " --> pdb=" O ASP u 90 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL u 92 " --> pdb=" O ALA u 74 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA u 74 " --> pdb=" O VAL u 92 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'v' and resid 45 through 47 removed outlier: 6.986A pdb=" N LYS v 78 " --> pdb=" O HIS v 46 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'v' and resid 51 through 53 Processing sheet with id= AT, first strand: chain 'w' and resid 13 through 17 Processing sheet with id= AU, first strand: chain 'w' and resid 34 through 40 removed outlier: 3.617A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'y' and resid 35 through 38 826 hydrogen bonds defined for protein. 2289 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2583 hydrogen bonds 4038 hydrogen bond angles 0 basepair planarities 1022 basepair parallelities 1534 stacking parallelities Total time for adding SS restraints: 134.52 Time building geometry restraints manager: 45.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6900 1.28 - 1.41: 37760 1.41 - 1.55: 45777 1.55 - 1.68: 5943 1.68 - 1.82: 147 Bond restraints: 96527 Sorted by residual: bond pdb=" C6 6MZ a2030 " pdb=" N6 6MZ a2030 " ideal model delta sigma weight residual 1.563 1.340 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C5 U a2449 " pdb=" C6 U a2449 " ideal model delta sigma weight residual 1.337 1.481 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C2 PSU a1917 " pdb=" N3 PSU a1917 " ideal model delta sigma weight residual 1.380 1.514 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C2 PSU a1911 " pdb=" N3 PSU a1911 " ideal model delta sigma weight residual 1.380 1.512 -0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C2 PSU a2504 " pdb=" N3 PSU a2504 " ideal model delta sigma weight residual 1.380 1.507 -0.127 2.00e-02 2.50e+03 4.00e+01 ... (remaining 96522 not shown) Histogram of bond angle deviations from ideal: 89.24 - 101.49: 1624 101.49 - 113.74: 74705 113.74 - 125.99: 58625 125.99 - 138.25: 9921 138.25 - 150.50: 6 Bond angle restraints: 144881 Sorted by residual: angle pdb=" C1' 6MZ a1618 " pdb=" N9 6MZ a1618 " pdb=" C8 6MZ a1618 " ideal model delta sigma weight residual 91.39 133.60 -42.21 3.00e+00 1.11e-01 1.98e+02 angle pdb=" C1' 1MG a 745 " pdb=" N9 1MG a 745 " pdb=" C8 1MG a 745 " ideal model delta sigma weight residual 100.16 141.32 -41.16 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C1' 6MZ a2030 " pdb=" N9 6MZ a2030 " pdb=" C8 6MZ a2030 " ideal model delta sigma weight residual 91.39 128.15 -36.76 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C1' 6MZ a1618 " pdb=" N9 6MZ a1618 " pdb=" C4 6MZ a1618 " ideal model delta sigma weight residual 154.15 118.54 35.61 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C1' 1MG a 745 " pdb=" N9 1MG a 745 " pdb=" C4 1MG a 745 " ideal model delta sigma weight residual 146.15 110.70 35.45 3.00e+00 1.11e-01 1.40e+02 ... (remaining 144876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 49438 35.05 - 70.10: 1653 70.10 - 105.15: 140 105.15 - 140.20: 9 140.20 - 175.25: 7 Dihedral angle restraints: 51247 sinusoidal: 41988 harmonic: 9259 Sorted by residual: dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 36.24 163.76 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' U a1758 " pdb=" C1' U a1758 " pdb=" N1 U a1758 " pdb=" C2 U a1758 " ideal model delta sinusoidal sigma weight residual -128.00 47.25 -175.25 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U a2689 " pdb=" C1' U a2689 " pdb=" N1 U a2689 " pdb=" C2 U a2689 " ideal model delta sinusoidal sigma weight residual -128.00 46.19 -174.19 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 51244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 17435 0.084 - 0.168: 937 0.168 - 0.252: 84 0.252 - 0.336: 8 0.336 - 0.421: 39 Chirality restraints: 18503 Sorted by residual: chirality pdb=" P C a 867 " pdb=" OP1 C a 867 " pdb=" OP2 C a 867 " pdb=" O5' C a 867 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" P G a2027 " pdb=" OP1 G a2027 " pdb=" OP2 G a2027 " pdb=" O5' G a2027 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" P U a 571 " pdb=" OP1 U a 571 " pdb=" OP2 U a 571 " pdb=" O5' U a 571 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 18500 not shown) Planarity restraints: 7409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M a2069 " 0.079 2.00e-02 2.50e+03 6.32e-01 8.98e+03 pdb=" C4' G7M a2069 " 0.460 2.00e-02 2.50e+03 pdb=" O4' G7M a2069 " 0.698 2.00e-02 2.50e+03 pdb=" C3' G7M a2069 " -0.603 2.00e-02 2.50e+03 pdb=" O3' G7M a2069 " -0.683 2.00e-02 2.50e+03 pdb=" C2' G7M a2069 " -0.167 2.00e-02 2.50e+03 pdb=" O2' G7M a2069 " 1.006 2.00e-02 2.50e+03 pdb=" C1' G7M a2069 " 0.200 2.00e-02 2.50e+03 pdb=" N9 G7M a2069 " -0.990 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 6MZ a1618 " 0.912 2.00e-02 2.50e+03 6.00e-01 8.11e+03 pdb=" C4' 6MZ a1618 " -0.199 2.00e-02 2.50e+03 pdb=" O4' 6MZ a1618 " -0.787 2.00e-02 2.50e+03 pdb=" C3' 6MZ a1618 " 0.234 2.00e-02 2.50e+03 pdb=" O3' 6MZ a1618 " -0.878 2.00e-02 2.50e+03 pdb=" C2' 6MZ a1618 " 0.611 2.00e-02 2.50e+03 pdb=" O2' 6MZ a1618 " 0.585 2.00e-02 2.50e+03 pdb=" C1' 6MZ a1618 " -0.457 2.00e-02 2.50e+03 pdb=" N9 6MZ a1618 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1835 " -0.025 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' 2MG a1835 " -0.467 2.00e-02 2.50e+03 pdb=" O4' 2MG a1835 " -0.881 2.00e-02 2.50e+03 pdb=" C3' 2MG a1835 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG a1835 " 0.508 2.00e-02 2.50e+03 pdb=" C2' 2MG a1835 " 0.293 2.00e-02 2.50e+03 pdb=" O2' 2MG a1835 " -0.797 2.00e-02 2.50e+03 pdb=" C1' 2MG a1835 " -0.162 2.00e-02 2.50e+03 pdb=" N9 2MG a1835 " 0.943 2.00e-02 2.50e+03 ... (remaining 7406 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 982 2.58 - 3.16: 70013 3.16 - 3.74: 175879 3.74 - 4.32: 238665 4.32 - 4.90: 330966 Nonbonded interactions: 816505 Sorted by model distance: nonbonded pdb=" OP1 U a1864 " pdb=" O2' G a2410 " model vdw 1.999 2.440 nonbonded pdb=" OP1 G a1296 " pdb=" O2' G a2709 " model vdw 2.002 2.440 nonbonded pdb=" OG SER e 15 " pdb=" OG1 THR e 18 " model vdw 2.004 2.440 nonbonded pdb=" OP2 G a1341 " pdb=" O2' U a1394 " model vdw 2.009 2.440 nonbonded pdb=" O2' G a2747 " pdb=" OG1 THR g 67 " model vdw 2.018 2.440 ... (remaining 816500 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 16.990 Check model and map are aligned: 1.360 Set scattering table: 0.810 Process input model: 318.940 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 359.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 0.007 0.223 96527 Z= 0.442 Angle : 0.845 42.208 144881 Z= 0.434 Chirality : 0.048 0.421 18503 Planarity : 0.026 0.632 7409 Dihedral : 14.480 175.248 45279 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.26 % Rotamer: Outliers : 1.62 % Allowed : 27.19 % Favored : 71.19 % 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: -0.03 (0.14), residues: 3206 helix: 0.99 (0.17), residues: 883 sheet: -0.44 (0.20), residues: 658 loop : -0.29 (0.15), residues: 1665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 872 time to evaluate : 3.783 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 outliers start: 43 outliers final: 22 residues processed: 889 average time/residue: 1.7886 time to fit residues: 2136.2078 Evaluate side-chains 854 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 832 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 12 residues processed: 13 average time/residue: 0.8301 time to fit residues: 22.8804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 511 optimal weight: 0.9980 chunk 459 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 chunk 474 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 353 optimal weight: 7.9990 chunk 550 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 1 13 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 86 ASN c 239 ASN d 94 GLN d 130 GLN d 150 GLN e 195 GLN f 37 ASN g 139 GLN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 ASN i 135 GLN ** n 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 77 HIS ** q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 66 GLN ** u 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 45 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 96527 Z= 0.407 Angle : 0.713 14.267 144881 Z= 0.385 Chirality : 0.040 0.380 18503 Planarity : 0.007 0.130 7409 Dihedral : 13.462 174.486 38865 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 5.88 % Allowed : 23.77 % Favored : 70.36 % 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: -0.06 (0.15), residues: 3206 helix: 1.04 (0.17), residues: 865 sheet: -0.48 (0.20), residues: 652 loop : -0.35 (0.15), residues: 1689 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 847 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 87 residues processed: 907 average time/residue: 1.7473 time to fit residues: 2141.0033 Evaluate side-chains 898 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 811 time to evaluate : 3.834 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 34 residues processed: 56 average time/residue: 0.9410 time to fit residues: 93.6865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 305 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 458 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 551 optimal weight: 7.9990 chunk 595 optimal weight: 8.9990 chunk 490 optimal weight: 0.9990 chunk 546 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 442 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS c 239 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 94 GLN d 130 GLN e 62 GLN e 195 GLN f 5 HIS g 20 ASN g 143 GLN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 28 ASN i 58 ASN ** j 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 98 GLN ** q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 GLN t 66 GLN u 88 HIS x 45 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 96527 Z= 0.296 Angle : 0.650 13.329 144881 Z= 0.357 Chirality : 0.036 0.372 18503 Planarity : 0.007 0.128 7409 Dihedral : 13.389 175.330 38865 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 5.69 % Allowed : 26.21 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3206 helix: 1.07 (0.17), residues: 870 sheet: -0.48 (0.19), residues: 704 loop : -0.34 (0.15), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 845 time to evaluate : 3.783 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 outliers start: 151 outliers final: 81 residues processed: 909 average time/residue: 1.7973 time to fit residues: 2208.8520 Evaluate side-chains 907 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 826 time to evaluate : 4.734 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 34 residues processed: 49 average time/residue: 0.8612 time to fit residues: 78.2824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 544 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 370 optimal weight: 6.9990 chunk 553 optimal weight: 5.9990 chunk 585 optimal weight: 8.9990 chunk 289 optimal weight: 10.0000 chunk 524 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: