Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 18:11:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/10_2023/7v2o_31658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/10_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_31658/10_2023/7v2o_31658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/10_2023/7v2o_31658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/10_2023/7v2o_31658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2o_31658/10_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 21.21, per 1000 atoms: 0.40 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: 20.91 Conformation dependent library (CDL) restraints added in 2.7 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: 17.08 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: 39.34 Time building geometry restraints manager: 22.59 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: 1.210 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: 0.030 Extract box with map and model: 8.940 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 146.270 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.140 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.780 ------------------------------------------------------------------------------- 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 % Allowed : 3.81 % Favored : 96.01 % 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 : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 337 average time/residue: 0.5407 time to fit residues: 301.3626 Evaluate side-chains 233 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 2.719 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3604 time to fit residues: 3.6876 ------------------------------------------------------------------------------- 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: 0.8257 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 57147 Z= 0.186 Angle : 0.550 8.362 84528 Z= 0.283 Chirality : 0.035 0.389 10595 Planarity : 0.004 0.046 5198 Dihedral : 16.214 179.717 20838 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.49 % Favored : 95.39 % Rotamer: Outliers : 1.04 % Allowed : 9.85 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2582 helix: 1.18 (0.16), residues: 1034 sheet: -0.06 (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 271 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 2.711 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 262 average time/residue: 0.5222 time to fit residues: 231.7545 Evaluate side-chains 228 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 2.711 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3695 time to fit residues: 11.5735 ------------------------------------------------------------------------------- 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: 10.0000 chunk 113 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 364 optimal weight: 0.5980 chunk 394 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 292 optimal weight: 2.9990 overall best weight: 6.7190 ------------------------------------------------------------------------------- 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 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 ** 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: 0.8322 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 57147 Z= 0.388 Angle : 0.690 9.124 84528 Z= 0.348 Chirality : 0.041 0.359 10595 Planarity : 0.006 0.048 5198 Dihedral : 16.569 179.276 20838 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 2.00 % Allowed : 12.62 % Favored : 85.38 % 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: -0.36 (0.16), residues: 2582 helix: 0.93 (0.16), residues: 1031 sheet: -0.43 (0.24), residues: 460 loop : -1.26 (0.19), residues: 1091 *********************** 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 271 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 2.789 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 257 average time/residue: 0.5264 time to fit residues: 230.2788 Evaluate side-chains 230 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 2.796 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3906 time to fit residues: 20.0118 ------------------------------------------------------------------------------- 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: 4.9990 chunk 189 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 chunk 366 optimal weight: 10.0000 chunk 387 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 57147 Z= 0.244 Angle : 0.592 11.216 84528 Z= 0.303 Chirality : 0.037 0.360 10595 Planarity : 0.004 0.050 5198 Dihedral : 16.396 179.166 20838 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 1.59 % Allowed : 14.66 % Favored : 83.75 % 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: -0.22 (0.17), residues: 2582 helix: 1.11 (0.16), residues: 1031 sheet: -0.40 (0.24), residues: 453 loop : -1.21 (0.19), 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 265 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 230 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 256 average time/residue: 0.5073 time to fit residues: 221.9797 Evaluate side-chains 236 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 2.691 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3871 time to fit residues: 16.1588 ------------------------------------------------------------------------------- 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: 5.9990 chunk 220 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 330 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 347 optimal weight: 5.9990 chunk 97 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1857 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= 0.263 Angle : 0.602 15.575 84528 Z= 0.306 Chirality : 0.037 0.356 10595 Planarity : 0.005 0.046 5198 Dihedral : 16.370 179.208 20838 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 1.54 % Allowed : 16.84 % Favored : 81.62 % 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: -0.17 (0.17), residues: 2582 helix: 1.10 (0.16), residues: 1045 sheet: -0.43 (0.24), residues: 451 loop : -1.14 (0.19), residues: 1086 *********************** 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 271 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 237 time to evaluate : 2.693 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 261 average time/residue: 0.5237 time to fit residues: 232.1450 Evaluate side-chains 233 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 216 time to evaluate : 2.692 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4075 time to fit residues: 15.7528 ------------------------------------------------------------------------------- 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: 0.9980 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: 1.9990 chunk 179 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 GLN E 130 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN K 13 GLN Q 93 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1985 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= 0.282 Angle : 0.615 14.488 84528 Z= 0.312 Chirality : 0.038 0.342 10595 Planarity : 0.005 0.052 5198 Dihedral : 16.380 179.374 20838 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 1.41 % Allowed : 17.34 % Favored : 81.25 % 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: -0.23 (0.17), residues: 2582 helix: 1.00 (0.16), residues: 1051 sheet: -0.39 (0.24), residues: 456 loop : -1.17 (0.19), residues: 1075 *********************** 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 261 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 230 time to evaluate : 2.764 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 247 average time/residue: 0.5210 time to fit residues: 220.6068 Evaluate side-chains 234 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 2.707 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4005 time to fit residues: 15.7107 ------------------------------------------------------------------------------- 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: 3.9990 chunk 219 optimal weight: 2.9990 chunk 326 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 386 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** U 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 57147 Z= 0.252 Angle : 0.594 14.150 84528 Z= 0.302 Chirality : 0.037 0.339 10595 Planarity : 0.004 0.049 5198 Dihedral : 16.330 179.819 20838 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 1.23 % Allowed : 18.16 % Favored : 80.62 % 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: 1.08 (0.16), residues: 1047 sheet: -0.43 (0.25), residues: 444 loop : -1.15 (0.19), residues: 1091 *********************** 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 264 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 237 time to evaluate : 2.724 Fit side-chains outliers start: 27 outliers final: 11 residues processed: 259 average time/residue: 0.5201 time to fit residues: 230.2947 Evaluate side-chains 231 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 2.703 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4077 time to fit residues: 11.2589 ------------------------------------------------------------------------------- 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: 7.9990 chunk 230 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 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: 5.7788 ------------------------------------------------------------------------------- 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 ** 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: 0.8313 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 57147 Z= 0.334 Angle : 0.649 15.829 84528 Z= 0.328 Chirality : 0.039 0.330 10595 Planarity : 0.005 0.052 5198 Dihedral : 16.427 179.414 20838 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 0.68 % Allowed : 18.88 % Favored : 80.44 % 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: -0.35 (0.17), residues: 2582 helix: 0.95 (0.16), residues: 1042 sheet: -0.52 (0.24), residues: 454 loop : -1.23 (0.19), residues: 1086 *********************** 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 248 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 2.772 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 245 average time/residue: 0.5469 time to fit residues: 228.3930 Evaluate side-chains 232 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 2.708 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4101 time to fit residues: 9.7794 ------------------------------------------------------------------------------- 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: 8.9990 chunk 370 optimal weight: 10.0000 chunk 337 optimal weight: 7.9990 chunk 360 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 325 optimal weight: 8.9990 chunk 340 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 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: 0.8305 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 57147 Z= 0.275 Angle : 0.619 15.428 84528 Z= 0.315 Chirality : 0.038 0.329 10595 Planarity : 0.005 0.052 5198 Dihedral : 16.402 179.161 20838 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 0.50 % Allowed : 19.11 % Favored : 80.39 % 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: -0.34 (0.17), residues: 2582 helix: 0.97 (0.16), residues: 1043 sheet: -0.58 (0.25), residues: 450 loop : -1.21 (0.19), residues: 1089 *********************** 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 243 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 232 time to evaluate : 2.739 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 240 average time/residue: 0.5292 time to fit residues: 216.8607 Evaluate side-chains 225 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 2.673 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3915 time to fit residues: 5.9388 ------------------------------------------------------------------------------- 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: 20.0000 chunk 380 optimal weight: 0.1980 chunk 232 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 399 optimal weight: 8.9990 chunk 367 optimal weight: 3.9990 chunk 318 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- 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 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 57147 Z= 0.297 Angle : 0.632 17.345 84528 Z= 0.321 Chirality : 0.038 0.322 10595 Planarity : 0.005 0.051 5198 Dihedral : 16.404 179.190 20838 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 0.59 % Allowed : 19.66 % Favored : 79.75 % 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: -0.36 (0.17), residues: 2582 helix: 0.92 (0.16), residues: 1044 sheet: -0.55 (0.25), residues: 441 loop : -1.20 (0.19), residues: 1097 ********************** 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 237 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 2.894 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 232 average time/residue: 0.5290 time to fit residues: 208.6681 Evaluate side-chains 227 residues out of total 2203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 2.709 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4430 time to fit residues: 8.5490 ------------------------------------------------------------------------------- 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: 8.9990 chunk 338 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 293 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 327 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.045058 restraints weight = 240714.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045165 restraints weight = 174811.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.045182 restraints weight = 129514.075| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 57147 Z= 0.334 Angle : 0.658 17.153 84528 Z= 0.332 Chirality : 0.040 0.317 10595 Planarity : 0.005 0.052 5198 Dihedral : 16.463 179.298 20838 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.26 % Rotamer: Outliers : 0.23 % Allowed : 20.15 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2582 helix: 0.79 (0.16), residues: 1043 sheet: -0.59 (0.25), residues: 455 loop : -1.22 (0.19), residues: 1084 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5533.05 seconds wall clock time: 102 minutes 23.71 seconds (6143.71 seconds total)