Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 11:30:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/08_2023/7v2o_31658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/08_2023/7v2o_31658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/08_2023/7v2o_31658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/08_2023/7v2o_31658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/08_2023/7v2o_31658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/08_2023/7v2o_31658.pdb" } resolution = 3.5 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= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1487 5.49 5 S 55 5.16 5 C 27488 2.51 5 N 9969 2.21 5 O 14004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 117": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 76": "OE1" <-> "OE2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 38": "OE1" <-> "OE2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "U PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 53005 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 31966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1487, 31966 Classifications: {'RNA': 1487} Modifications used: {'rna2p_pur': 125, 'rna2p_pyr': 97, 'rna3p_pur': 718, 'rna3p_pyr': 547} Link IDs: {'rna2p': 222, 'rna3p': 1264} Chain breaks: 3 Chain: "B" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1802 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "F" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 794 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "K" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "M" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 905 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "N" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 682 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "Q" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 834 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "S" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "T" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "U" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 12, 'TRANS': 251} Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35439 SG CYS D 9 95.611 74.246 91.599 1.00 74.31 S ATOM 35464 SG CYS D 12 96.561 77.050 93.951 1.00 75.48 S ATOM 35582 SG CYS D 26 98.416 73.405 92.745 1.00 80.60 S ATOM 35622 SG CYS D 31 99.505 76.143 91.542 1.00 89.50 S ATOM 46200 SG CYS N 24 67.440 121.098 48.829 1.00 73.42 S ATOM 46224 SG CYS N 27 66.084 119.588 52.189 1.00 74.93 S ATOM 46331 SG CYS N 40 66.490 123.441 51.744 1.00 70.43 S ATOM 46356 SG CYS N 43 69.455 121.118 51.947 1.00 70.47 S Time building chain proxies: 19.59, per 1000 atoms: 0.37 Number of scatterers: 53005 At special positions: 0 Unit cell: (146.28, 213.9, 223.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 55 16.00 P 1487 15.00 O 14004 8.00 N 9969 7.00 C 27488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.52 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 12 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 12 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4854 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 22 sheets defined 43.6% alpha, 18.6% beta 461 base pairs and 738 stacking pairs defined. Time for finding SS restraints: 18.61 Creating SS restraints... Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.674A pdb=" N GLY B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.361A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 65 Processing helix chain 'B' and resid 76 through 87 removed outlier: 4.538A pdb=" N ILE B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.504A pdb=" N ILE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.508A pdb=" N GLN B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.554A pdb=" N LEU B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.889A pdb=" N ILE B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.845A pdb=" N LEU C 12 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 72 through 78 removed outlier: 4.211A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 removed outlier: 3.764A pdb=" N SER C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 4.080A pdb=" N GLY C 159 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.728A pdb=" N ALA C 180 " --> pdb=" O THR C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.610A pdb=" N CYS D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.757A pdb=" N TYR D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 113 through 123 Processing helix chain 'D' and resid 151 through 154 removed outlier: 4.268A pdb=" N ASN D 154 " --> pdb=" O LYS D 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 154' Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 199 through 209 removed outlier: 4.005A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.694A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 141 Processing helix chain 'E' and resid 144 through 153 Processing helix chain 'F' and resid 15 through 33 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 71 through 80 Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.587A pdb=" N THR G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.625A pdb=" N VAL G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.634A pdb=" N GLN G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 145 Processing helix chain 'G' and resid 148 through 154 removed outlier: 3.721A pdb=" N HIS G 153 " --> pdb=" O ALA G 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 18 Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.802A pdb=" N ILE H 100 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'I' and resid 33 through 37 Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 43 through 53 removed outlier: 4.098A pdb=" N LEU I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) Proline residue: I 49 - end of helix removed outlier: 3.895A pdb=" N VAL I 53 " --> pdb=" O PRO I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'J' and resid 12 through 30 Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'K' and resid 45 through 49 removed outlier: 3.616A pdb=" N GLY K 49 " --> pdb=" O GLY K 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 49' Processing helix chain 'K' and resid 51 through 56 removed outlier: 3.692A pdb=" N ARG K 54 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY K 56 " --> pdb=" O SER K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 74 removed outlier: 3.813A pdb=" N ALA K 74 " --> pdb=" O LYS K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 100 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'M' and resid 14 through 20 Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.977A pdb=" N ASN M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.513A pdb=" N ILE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.716A pdb=" N HIS O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 removed outlier: 3.515A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 63 removed outlier: 3.700A pdb=" N ALA P 56 " --> pdb=" O ASP P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 76 Processing helix chain 'Q' and resid 81 through 94 removed outlier: 4.119A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.693A pdb=" N SER Q 99 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 44 removed outlier: 4.065A pdb=" N ARG R 42 " --> pdb=" O GLU R 38 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 57 Processing helix chain 'R' and resid 59 through 77 Processing helix chain 'S' and resid 12 through 25 removed outlier: 5.117A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS S 25 " --> pdb=" O GLU S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 75 removed outlier: 3.803A pdb=" N PHE S 74 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 46 removed outlier: 3.720A pdb=" N ARG T 17 " --> pdb=" O LEU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 69 removed outlier: 3.753A pdb=" N ALA T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 93 Processing helix chain 'U' and resid 33 through 44 Processing helix chain 'U' and resid 60 through 68 removed outlier: 3.810A pdb=" N LYS U 68 " --> pdb=" O GLU U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 90 removed outlier: 3.585A pdb=" N ILE U 85 " --> pdb=" O ARG U 81 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU U 86 " --> pdb=" O LEU U 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP U 88 " --> pdb=" O PRO U 84 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR U 89 " --> pdb=" O ILE U 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU U 90 " --> pdb=" O LEU U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 116 removed outlier: 3.596A pdb=" N ILE U 112 " --> pdb=" O VAL U 108 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE U 116 " --> pdb=" O ILE U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 129 through 143 Proline residue: U 135 - end of helix Processing helix chain 'U' and resid 156 through 163 Processing helix chain 'U' and resid 172 through 182 removed outlier: 3.742A pdb=" N PHE U 180 " --> pdb=" O ILE U 176 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR U 181 " --> pdb=" O ALA U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 232 Processing helix chain 'U' and resid 238 through 247 removed outlier: 3.738A pdb=" N ASN U 245 " --> pdb=" O ASN U 241 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 247 through 253 Processing helix chain 'U' and resid 256 through 264 removed outlier: 3.723A pdb=" N VAL U 260 " --> pdb=" O THR U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 276 through 289 removed outlier: 3.750A pdb=" N LYS U 289 " --> pdb=" O ASN U 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 16 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20 removed outlier: 5.136A pdb=" N HIS B 40 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 34 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 8.131A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE B 162 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 184 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 21 removed outlier: 3.872A pdb=" N ARG C 59 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN C 102 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLN C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL C 68 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 171 removed outlier: 3.619A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 5.244A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU E 12 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY E 23 " --> pdb=" O GLN E 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.533A pdb=" N SER E 87 " --> pdb=" O PHE E 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 52 removed outlier: 7.332A pdb=" N GLU F 38 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N GLU F 66 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL F 40 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLN F 64 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU F 42 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TRP F 62 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY F 58 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 48 " --> pdb=" O PRO F 56 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG F 87 " --> pdb=" O VAL F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 73 through 80 Processing sheet with id=AB1, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.598A pdb=" N GLY H 47 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 83 through 85 Processing sheet with id=AB3, first strand: chain 'H' and resid 83 through 85 removed outlier: 6.073A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS H 135 " --> pdb=" O ILE H 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.602A pdb=" N THR I 64 " --> pdb=" O ARG I 16 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR I 27 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL I 65 " --> pdb=" O THR I 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 38 through 49 removed outlier: 6.849A pdb=" N LEU J 71 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG J 43 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY J 10 " --> pdb=" O HIS J 68 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU J 95 " --> pdb=" O ARG J 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 38 through 49 removed outlier: 6.849A pdb=" N LEU J 71 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG J 43 " --> pdb=" O THR J 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 39 through 44 removed outlier: 3.646A pdb=" N THR K 41 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY K 17 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE K 83 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL K 80 " --> pdb=" O VAL K 105 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER K 107 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 62 through 64 removed outlier: 6.390A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 49 through 51 removed outlier: 6.122A pdb=" N ILE P 19 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR P 17 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL P 2 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 5 through 15 removed outlier: 14.464A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.787A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP Q 13 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR Q 18 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N LYS Q 69 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU Q 43 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU Q 74 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE Q 60 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU Q 76 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP Q 55 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 31 through 33 removed outlier: 3.901A pdb=" N THR S 33 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 96 through 100 removed outlier: 6.348A pdb=" N VAL U 73 " --> pdb=" O THR U 97 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE U 99 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA U 75 " --> pdb=" O ILE U 99 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE U 55 " --> pdb=" O VAL U 125 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL U 124 " --> pdb=" O VAL U 151 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N MET U 153 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA U 126 " --> pdb=" O MET U 153 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N GLN U 155 " --> pdb=" O ALA U 126 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU U 154 " --> pdb=" O ALA U 204 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER U 203 " --> pdb=" O VAL U 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL U 205 " --> pdb=" O MET U 188 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET U 188 " --> pdb=" O VAL U 205 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG U 207 " --> pdb=" O THR U 186 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR U 186 " --> pdb=" O ARG U 207 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1219 hydrogen bonds 1992 hydrogen bond angles 0 basepair planarities 461 basepair parallelities 738 stacking parallelities Total time for adding SS restraints: 46.34 Time building geometry restraints manager: 23.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9059 1.34 - 1.46: 24577 1.46 - 1.58: 20445 1.58 - 1.70: 2970 1.70 - 1.82: 96 Bond restraints: 57147 Sorted by residual: bond pdb=" C TYR D 38 " pdb=" N PRO D 39 " ideal model delta sigma weight residual 1.331 1.359 -0.027 8.70e-03 1.32e+04 9.80e+00 bond pdb=" C ARG D 36 " pdb=" N PRO D 37 " ideal model delta sigma weight residual 1.334 1.357 -0.023 8.40e-03 1.42e+04 7.58e+00 bond pdb=" N GLY V 2 " pdb=" CA GLY V 2 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 7.02e+00 bond pdb=" CA PRO D 39 " pdb=" C PRO D 39 " ideal model delta sigma weight residual 1.514 1.528 -0.014 5.50e-03 3.31e+04 6.64e+00 bond pdb=" O5' G A 243 " pdb=" C5' G A 243 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.26e+00 ... (remaining 57142 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.69: 7263 105.69 - 112.91: 31180 112.91 - 120.13: 24985 120.13 - 127.35: 17721 127.35 - 134.57: 3379 Bond angle restraints: 84528 Sorted by residual: angle pdb=" O3' G A1426 " pdb=" C3' G A1426 " pdb=" C2' G A1426 " ideal model delta sigma weight residual 109.50 118.27 -8.77 1.50e+00 4.44e-01 3.42e+01 angle pdb=" O3' U A1061 " pdb=" C3' U A1061 " pdb=" C2' U A1061 " ideal model delta sigma weight residual 113.70 122.04 -8.34 1.50e+00 4.44e-01 3.09e+01 angle pdb=" O3' U A 735 " pdb=" C3' U A 735 " pdb=" C2' U A 735 " ideal model delta sigma weight residual 109.50 117.74 -8.24 1.50e+00 4.44e-01 3.02e+01 angle pdb=" O3' A A 156 " pdb=" C3' A A 156 " pdb=" C2' A A 156 " ideal model delta sigma weight residual 113.70 121.75 -8.05 1.50e+00 4.44e-01 2.88e+01 angle pdb=" C4' U A 82 " pdb=" C3' U A 82 " pdb=" O3' U A 82 " ideal model delta sigma weight residual 109.40 117.44 -8.04 1.50e+00 4.44e-01 2.87e+01 ... (remaining 84523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 29731 35.94 - 71.88: 1272 71.88 - 107.82: 101 107.82 - 143.76: 13 143.76 - 179.70: 23 Dihedral angle restraints: 31140 sinusoidal: 23596 harmonic: 7544 Sorted by residual: dihedral pdb=" C5' U A 735 " pdb=" C4' U A 735 " pdb=" C3' U A 735 " pdb=" O3' U A 735 " ideal model delta sinusoidal sigma weight residual 147.00 75.38 71.62 1 8.00e+00 1.56e-02 1.03e+02 dihedral pdb=" C4' U A 735 " pdb=" C3' U A 735 " pdb=" C2' U A 735 " pdb=" C1' U A 735 " ideal model delta sinusoidal sigma weight residual -35.00 32.74 -67.74 1 8.00e+00 1.56e-02 9.32e+01 dihedral pdb=" O4' U A1176 " pdb=" C1' U A1176 " pdb=" N1 U A1176 " pdb=" C2 U A1176 " ideal model delta sinusoidal sigma weight residual -160.00 17.66 -177.66 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 31137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 6974 0.105 - 0.210: 3002 0.210 - 0.314: 609 0.314 - 0.419: 7 0.419 - 0.524: 3 Chirality restraints: 10595 Sorted by residual: chirality pdb=" C3' G A1426 " pdb=" C4' G A1426 " pdb=" O3' G A1426 " pdb=" C2' G A1426 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.52 2.00e-01 2.50e+01 6.86e+00 chirality pdb=" C3' A A1497 " pdb=" C4' A A1497 " pdb=" O3' A A1497 " pdb=" C2' A A1497 " both_signs ideal model delta sigma weight residual False -2.74 -2.29 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" C3' U A 735 " pdb=" C4' U A 735 " pdb=" O3' U A 735 " pdb=" C2' U A 735 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 10592 not shown) Planarity restraints: 5198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A1459 " 0.036 2.00e-02 2.50e+03 1.83e-02 7.52e+00 pdb=" N1 U A1459 " -0.036 2.00e-02 2.50e+03 pdb=" C2 U A1459 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U A1459 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U A1459 " 0.006 2.00e-02 2.50e+03 pdb=" C4 U A1459 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U A1459 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U A1459 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U A1459 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 982 " 0.024 2.00e-02 2.50e+03 1.18e-02 4.16e+00 pdb=" N9 G A 982 " -0.030 2.00e-02 2.50e+03 pdb=" C8 G A 982 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G A 982 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 982 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 982 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G A 982 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G A 982 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 982 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 982 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 982 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G A 982 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1017 " 0.025 2.00e-02 2.50e+03 1.16e-02 4.03e+00 pdb=" N9 G A1017 " -0.026 2.00e-02 2.50e+03 pdb=" C8 G A1017 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A1017 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G A1017 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G A1017 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A1017 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G A1017 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G A1017 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G A1017 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G A1017 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A1017 " 0.002 2.00e-02 2.50e+03 ... (remaining 5195 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5322 2.74 - 3.28: 47961 3.28 - 3.82: 107368 3.82 - 4.36: 130669 4.36 - 4.90: 181486 Nonbonded interactions: 472806 Sorted by model distance: nonbonded pdb=" O2' G A 434 " pdb=" O4 U A 479 " model vdw 2.203 2.440 nonbonded pdb=" OP1 C A 685 " pdb=" O2' A A 686 " model vdw 2.211 2.440 nonbonded pdb=" O GLY I 67 " pdb=" NE2 GLN I 73 " model vdw 2.244 2.520 nonbonded pdb=" O2' A A 144 " pdb=" O4' C A 145 " model vdw 2.252 2.440 nonbonded pdb=" O2' A A1251 " pdb=" O2' C A1307 " model vdw 2.257 2.440 ... (remaining 472801 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 11.480 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 154.830 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.008 0.042 57147 Z= 0.489 Angle : 1.117 8.823 84528 Z= 0.706 Chirality : 0.104 0.524 10595 Planarity : 0.003 0.021 5198 Dihedral : 16.739 179.697 26286 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.08 % 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: -0.53 (0.16), residues: 2582 helix: 0.70 (0.16), residues: 1010 sheet: -0.02 (0.26), residues: 377 loop : -1.38 (0.17), residues: 1195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 334 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 337 average time/residue: 0.5434 time to fit residues: 301.6323 Evaluate side-chains 233 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 2.711 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3633 time to fit residues: 3.7349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 338 optimal weight: 0.0470 chunk 303 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 314 optimal weight: 0.1980 chunk 121 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 364 optimal weight: 4.9990 overall best weight: 2.6484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 108 ASN D 160 GLN F 13 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN I 89 ASN J 13 HIS J 76 ASN K 13 GLN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 57147 Z= 0.192 Angle : 0.557 8.382 84528 Z= 0.286 Chirality : 0.035 0.393 10595 Planarity : 0.004 0.047 5198 Dihedral : 16.211 179.648 20838 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.38 % Favored : 95.51 % Rotamer Outliers : 1.04 % 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: -0.08 (0.16), residues: 2582 helix: 1.18 (0.16), residues: 1034 sheet: -0.05 (0.25), residues: 428 loop : -1.22 (0.18), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 2.815 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 258 average time/residue: 0.5237 time to fit residues: 227.8389 Evaluate side-chains 226 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 2.695 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3653 time to fit residues: 10.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 202 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 364 optimal weight: 4.9990 chunk 394 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 chunk 361 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 160 GLN F 13 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 106 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN U 226 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.082 57147 Z= 0.461 Angle : 0.749 9.174 84528 Z= 0.376 Chirality : 0.044 0.382 10595 Planarity : 0.006 0.051 5198 Dihedral : 16.687 179.736 20838 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer Outliers : 2.13 % 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: -0.52 (0.16), residues: 2582 helix: 0.76 (0.16), residues: 1031 sheet: -0.47 (0.24), residues: 465 loop : -1.32 (0.19), residues: 1086 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 225 time to evaluate : 2.694 Fit side-chains outliers start: 47 outliers final: 30 residues processed: 258 average time/residue: 0.5190 time to fit residues: 227.4917 Evaluate side-chains 236 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 206 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3863 time to fit residues: 24.9405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 360 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 174 optimal weight: 0.1980 chunk 244 optimal weight: 0.9990 chunk 366 optimal weight: 9.9990 chunk 387 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 346 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 160 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN U 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 57147 Z= 0.149 Angle : 0.547 9.015 84528 Z= 0.281 Chirality : 0.035 0.369 10595 Planarity : 0.004 0.048 5198 Dihedral : 16.275 179.989 20838 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer Outliers : 1.27 % 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: -0.09 (0.17), residues: 2582 helix: 1.21 (0.16), residues: 1040 sheet: -0.22 (0.25), residues: 444 loop : -1.22 (0.18), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 256 average time/residue: 0.5534 time to fit residues: 241.8526 Evaluate side-chains 227 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 2.698 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3985 time to fit residues: 13.7054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 322 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 330 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN D 160 GLN E 130 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 57147 Z= 0.275 Angle : 0.599 10.349 84528 Z= 0.304 Chirality : 0.037 0.357 10595 Planarity : 0.005 0.044 5198 Dihedral : 16.317 179.332 20838 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2582 helix: 1.18 (0.16), residues: 1040 sheet: -0.37 (0.25), residues: 449 loop : -1.12 (0.19), residues: 1093 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 2.711 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 244 average time/residue: 0.5229 time to fit residues: 217.8448 Evaluate side-chains 227 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 2.704 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4190 time to fit residues: 13.7871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 130 optimal weight: 20.0000 chunk 349 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 387 optimal weight: 30.0000 chunk 322 optimal weight: 0.8980 chunk 179 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 203 optimal weight: 0.4980 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN K 13 GLN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 57147 Z= 0.264 Angle : 0.601 16.064 84528 Z= 0.305 Chirality : 0.037 0.349 10595 Planarity : 0.004 0.050 5198 Dihedral : 16.326 179.409 20838 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.31 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2582 helix: 1.14 (0.16), residues: 1039 sheet: -0.40 (0.24), residues: 456 loop : -1.16 (0.19), residues: 1087 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 2.941 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 244 average time/residue: 0.5286 time to fit residues: 218.2100 Evaluate side-chains 229 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 2.697 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4346 time to fit residues: 17.4415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 374 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 326 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 386 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 57147 Z= 0.224 Angle : 0.577 15.059 84528 Z= 0.293 Chirality : 0.036 0.341 10595 Planarity : 0.004 0.048 5198 Dihedral : 16.251 179.611 20838 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2582 helix: 1.20 (0.16), residues: 1040 sheet: -0.36 (0.25), residues: 444 loop : -1.14 (0.19), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 2.722 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 243 average time/residue: 0.5354 time to fit residues: 219.9435 Evaluate side-chains 225 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 2.700 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3901 time to fit residues: 9.6792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 239 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 303 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 57147 Z= 0.314 Angle : 0.634 14.369 84528 Z= 0.321 Chirality : 0.038 0.329 10595 Planarity : 0.005 0.050 5198 Dihedral : 16.360 179.616 20838 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer Outliers : 0.45 % 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: -0.25 (0.17), residues: 2582 helix: 1.09 (0.16), residues: 1039 sheet: -0.50 (0.24), residues: 456 loop : -1.22 (0.19), residues: 1087 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 227 time to evaluate : 2.768 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 235 average time/residue: 0.5423 time to fit residues: 216.2299 Evaluate side-chains 225 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 219 time to evaluate : 2.707 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3751 time to fit residues: 7.4093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 351 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 360 optimal weight: 0.4980 chunk 216 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 340 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 57147 Z= 0.211 Angle : 0.573 17.175 84528 Z= 0.292 Chirality : 0.036 0.324 10595 Planarity : 0.004 0.050 5198 Dihedral : 16.219 179.924 20838 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer Outliers : 0.50 % 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: -0.13 (0.17), residues: 2582 helix: 1.22 (0.16), residues: 1041 sheet: -0.47 (0.25), residues: 450 loop : -1.17 (0.19), residues: 1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 2.738 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 245 average time/residue: 0.5345 time to fit residues: 220.7576 Evaluate side-chains 222 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5369 time to fit residues: 7.4876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 236 optimal weight: 0.2980 chunk 380 optimal weight: 30.0000 chunk 232 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 367 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 57147 Z= 0.277 Angle : 0.613 17.239 84528 Z= 0.311 Chirality : 0.037 0.312 10595 Planarity : 0.005 0.048 5198 Dihedral : 16.274 178.603 20838 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.69 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2582 helix: 1.14 (0.16), residues: 1038 sheet: -0.45 (0.25), residues: 437 loop : -1.19 (0.19), residues: 1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 2.803 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 229 average time/residue: 0.5307 time to fit residues: 206.8173 Evaluate side-chains 223 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 2.772 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3873 time to fit residues: 5.3605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 252 optimal weight: 7.9990 chunk 338 optimal weight: 0.6980 chunk 97 optimal weight: 40.0000 chunk 293 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 327 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 overall best weight: 5.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN U 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045193 restraints weight = 240818.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045307 restraints weight = 171361.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.045300 restraints weight = 135028.713| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 57147 Z= 0.343 Angle : 0.664 17.415 84528 Z= 0.335 Chirality : 0.040 0.296 10595 Planarity : 0.005 0.050 5198 Dihedral : 16.411 179.164 20838 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Rotamer Outliers : 0.32 % 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: -0.38 (0.17), residues: 2582 helix: 0.91 (0.16), residues: 1039 sheet: -0.54 (0.25), residues: 455 loop : -1.22 (0.19), residues: 1088 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5452.57 seconds wall clock time: 100 minutes 45.88 seconds (6045.88 seconds total)