Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 16:34:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/04_2023/7v2m_31656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/04_2023/7v2m_31656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/04_2023/7v2m_31656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/04_2023/7v2m_31656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/04_2023/7v2m_31656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/04_2023/7v2m_31656.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 1486 5.49 5 S 61 5.16 5 C 28920 2.51 5 N 10336 2.21 5 O 14424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "S GLU 21": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "U GLU 114": "OE1" <-> "OE2" Residue "U GLU 160": "OE1" <-> "OE2" Residue "W GLU 142": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 55229 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 31944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1486, 31944 Classifications: {'RNA': 1486} Modifications used: {'rna2p_pur': 130, 'rna2p_pyr': 100, 'rna3p_pur': 712, 'rna3p_pyr': 544} Link IDs: {'rna2p': 230, 'rna3p': 1255} 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: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2267 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} 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: "W" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2048 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} 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 35417 SG CYS D 9 97.172 70.836 96.041 1.00 43.08 S ATOM 35442 SG CYS D 12 98.247 73.869 98.313 1.00 44.89 S ATOM 35560 SG CYS D 26 100.348 70.105 97.006 1.00 47.66 S ATOM 35600 SG CYS D 31 101.305 72.873 95.448 1.00 52.54 S ATOM 46178 SG CYS N 24 70.105 123.080 48.627 1.00 57.07 S ATOM 46202 SG CYS N 27 68.216 121.714 51.520 1.00 55.08 S ATOM 46309 SG CYS N 40 69.401 125.363 51.733 1.00 52.03 S ATOM 46334 SG CYS N 43 72.030 122.763 51.830 1.00 54.35 S Time building chain proxies: 21.02, per 1000 atoms: 0.38 Number of scatterers: 55229 At special positions: 0 Unit cell: (149.04, 212.52, 227.7, 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 61 16.00 P 1486 15.00 O 14424 8.00 N 10336 7.00 C 28920 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: 21.27 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 26 " 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 12 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " Number of angles added : 12 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 24 sheets defined 43.7% alpha, 17.9% beta 475 base pairs and 756 stacking pairs defined. Time for finding SS restraints: 15.97 Creating SS restraints... Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.650A pdb=" N ALA B 13 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.312A 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: 4.412A pdb=" N ILE B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.663A pdb=" N GLN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 170 through 180 removed outlier: 3.505A pdb=" N LEU B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.678A pdb=" N ILE B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.805A pdb=" N LEU C 12 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 72 through 78 removed outlier: 4.113A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 82 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: 3.875A pdb=" N SER C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.981A pdb=" N GLY C 159 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.537A pdb=" N CYS D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.821A 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 150 through 154 removed outlier: 4.376A pdb=" N ASN D 154 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 200 through 209 removed outlier: 3.645A 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: 3.842A 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 removed outlier: 3.812A pdb=" N TYR F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.576A 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 68 removed outlier: 3.993A pdb=" N VAL G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 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: 3.961A 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 42 through 46 Processing helix chain 'I' and resid 47 through 53 removed outlier: 3.688A 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: 3.704A 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: 4.040A pdb=" N ARG K 54 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY K 56 " --> pdb=" O SER K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 74 removed outlier: 3.908A pdb=" N ALA K 74 " --> pdb=" O LYS K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 100 removed outlier: 3.537A pdb=" N ALA K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) 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 19 Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 48 removed outlier: 3.585A pdb=" N LEU M 48 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.846A pdb=" N ASN M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.905A 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 removed outlier: 3.541A pdb=" N LYS O 8 " --> pdb=" O THR O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 46 Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.644A pdb=" N HIS O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'Q' and resid 81 through 94 removed outlier: 3.960A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.520A pdb=" N SER Q 99 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 42 removed outlier: 3.527A pdb=" N LEU R 40 " --> pdb=" O ASN R 36 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG R 42 " --> pdb=" O GLU R 38 " (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 24 removed outlier: 4.945A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 69 removed outlier: 3.552A pdb=" N VAL S 67 " --> pdb=" O GLU S 64 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY S 68 " --> pdb=" O ASN S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.712A pdb=" N ARG T 17 " --> pdb=" O LEU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 69 removed outlier: 3.603A pdb=" N ALA T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 3.996A 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 9 through 15 Processing helix chain 'U' and resid 33 through 45 removed outlier: 3.538A pdb=" N GLU U 45 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 69 removed outlier: 3.684A pdb=" N ARG U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 87 Processing helix chain 'U' and resid 88 through 90 No H-bonds generated for 'chain 'U' and resid 88 through 90' Processing helix chain 'U' and resid 108 through 116 removed outlier: 3.713A pdb=" N GLU U 114 " --> pdb=" O SER U 110 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN U 115 " --> pdb=" O VAL U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 129 through 143 removed outlier: 4.003A pdb=" N THR U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) Proline residue: U 135 - end of helix Processing helix chain 'U' and resid 156 through 163 Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.742A pdb=" N VAL U 178 " --> pdb=" O LEU U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 195 removed outlier: 3.804A pdb=" N VAL U 194 " --> pdb=" O PRO U 191 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE U 195 " --> pdb=" O LYS U 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 191 through 195' Processing helix chain 'U' and resid 220 through 232 removed outlier: 3.815A pdb=" N PHE U 232 " --> pdb=" O ILE U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 245 removed outlier: 3.550A pdb=" N ASN U 245 " --> pdb=" O ASN U 241 " (cutoff:3.500A) Processing helix chain 'U' and resid 247 through 253 removed outlier: 3.609A pdb=" N GLN U 253 " --> pdb=" O GLU U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 261 removed outlier: 3.676A pdb=" N GLN U 259 " --> pdb=" O SER U 255 " (cutoff:3.500A) Processing helix chain 'U' and resid 276 through 290 removed outlier: 4.032A pdb=" N LYS U 289 " --> pdb=" O ASN U 285 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA U 290 " --> pdb=" O GLY U 286 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 16 Processing helix chain 'W' and resid 35 through 45 Processing helix chain 'W' and resid 60 through 68 removed outlier: 3.579A pdb=" N GLN W 65 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 90 Processing helix chain 'W' and resid 107 through 116 removed outlier: 3.682A pdb=" N VAL W 111 " --> pdb=" O ASP W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 143 removed outlier: 3.845A pdb=" N ILE W 137 " --> pdb=" O THR W 133 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU W 140 " --> pdb=" O ILE W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 156 through 163 Processing helix chain 'W' and resid 172 through 181 Processing helix chain 'W' and resid 220 through 232 removed outlier: 3.752A pdb=" N PHE W 232 " --> pdb=" O ILE W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 238 through 245 Processing helix chain 'W' and resid 253 through 264 removed outlier: 4.029A pdb=" N ILE W 257 " --> pdb=" O GLN W 253 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU W 258 " --> pdb=" O LYS W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 290 removed outlier: 3.950A pdb=" N TYR W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20 removed outlier: 5.037A pdb=" N HIS B 40 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE B 41 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 8.512A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 69 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.286A 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: 3.630A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.772A pdb=" N ASP D 144 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 146 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 182 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 5.138A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU E 12 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.916A 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 Processing sheet with id=AA8, first strand: chain 'F' and resid 37 through 41 removed outlier: 7.087A pdb=" N GLN F 64 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL F 40 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TRP F 62 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 37 through 41 removed outlier: 7.087A pdb=" N GLN F 64 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL F 40 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TRP F 62 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 73 through 76 Processing sheet with id=AB2, first strand: chain 'H' and resid 24 through 27 Processing sheet with id=AB3, first strand: chain 'H' and resid 94 through 95 removed outlier: 6.001A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.600A 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 Processing sheet with id=AB6, first strand: chain 'J' and resid 38 through 49 removed outlier: 4.482A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR J 42 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR J 67 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL J 44 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU J 65 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG J 46 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE J 63 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR J 48 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU J 61 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY J 10 " --> pdb=" O HIS J 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 38 through 49 removed outlier: 4.482A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR J 42 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR J 67 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL J 44 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU J 65 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG J 46 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE J 63 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR J 48 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU J 61 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 39 through 44 removed outlier: 6.176A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL K 109 " --> pdb=" O VAL K 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.632A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL L 36 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 2 through 11 removed outlier: 6.590A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 5 through 15 removed outlier: 14.826A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASP Q 13 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR Q 18 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 4.472A 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: 3.700A pdb=" N THR S 33 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 52 through 55 removed outlier: 7.062A pdb=" N VAL U 52 " --> pdb=" O VAL U 74 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE U 76 " --> pdb=" O VAL U 52 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU U 54 " --> pdb=" O PHE U 76 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL U 73 " --> pdb=" O THR U 97 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE U 99 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA U 75 " --> pdb=" O ILE U 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'U' and resid 123 through 126 removed outlier: 6.039A pdb=" N VAL U 124 " --> pdb=" O VAL U 151 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N MET U 153 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA U 126 " --> pdb=" O MET U 153 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N GLN U 155 " --> pdb=" O ALA U 126 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER U 203 " --> pdb=" O VAL U 190 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG U 207 " --> pdb=" O THR U 186 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N THR U 186 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE U 209 " --> pdb=" O ALA U 184 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA U 184 " --> pdb=" O ILE U 209 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 96 through 99 removed outlier: 6.666A pdb=" N VAL W 73 " --> pdb=" O THR W 97 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE W 99 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA W 75 " --> pdb=" O ILE W 99 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE W 55 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN W 127 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY W 149 " --> pdb=" O ILE W 122 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA W 126 " --> pdb=" O VAL W 151 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER W 203 " --> pdb=" O ILE W 189 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE W 189 " --> pdb=" O SER W 203 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL W 205 " --> pdb=" O VAL W 187 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 2943 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1257 hydrogen bonds 2052 hydrogen bond angles 0 basepair planarities 475 basepair parallelities 756 stacking parallelities Total time for adding SS restraints: 40.50 Time building geometry restraints manager: 23.02 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: 9947 1.34 - 1.46: 25347 1.46 - 1.58: 21033 1.58 - 1.70: 2968 1.70 - 1.83: 107 Bond restraints: 59402 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 9.93e+00 bond pdb=" O5' G A 980 " pdb=" C5' G A 980 " ideal model delta sigma weight residual 1.420 1.459 -0.039 1.50e-02 4.44e+03 6.82e+00 bond pdb=" O5' G A 243 " pdb=" C5' G A 243 " ideal model delta sigma weight residual 1.420 1.459 -0.039 1.50e-02 4.44e+03 6.82e+00 bond pdb=" CA PRO D 39 " pdb=" C PRO D 39 " ideal model delta sigma weight residual 1.514 1.529 -0.014 5.50e-03 3.31e+04 6.71e+00 bond pdb=" C TYR F 50 " pdb=" N PRO F 51 " ideal model delta sigma weight residual 1.333 1.359 -0.025 1.01e-02 9.80e+03 6.28e+00 ... (remaining 59397 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.23: 7096 105.23 - 112.57: 30883 112.57 - 119.91: 25563 119.91 - 127.25: 20494 127.25 - 134.58: 3537 Bond angle restraints: 87573 Sorted by residual: angle pdb=" O3' C A1308 " pdb=" C3' C A1308 " pdb=" C2' C A1308 " ideal model delta sigma weight residual 113.70 125.14 -11.44 1.50e+00 4.44e-01 5.82e+01 angle pdb=" O3' U A1484 " pdb=" C3' U A1484 " pdb=" C2' U A1484 " ideal model delta sigma weight residual 109.50 118.66 -9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" O3' A A 156 " pdb=" C3' A A 156 " pdb=" C2' A A 156 " ideal model delta sigma weight residual 113.70 122.65 -8.95 1.50e+00 4.44e-01 3.56e+01 angle pdb=" C4' A A1497 " pdb=" C3' A A1497 " pdb=" O3' A A1497 " ideal model delta sigma weight residual 109.40 117.85 -8.45 1.50e+00 4.44e-01 3.17e+01 angle pdb=" O3' G A 409 " pdb=" C3' G A 409 " pdb=" C2' G A 409 " ideal model delta sigma weight residual 109.50 117.74 -8.24 1.50e+00 4.44e-01 3.02e+01 ... (remaining 87568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 31208 35.91 - 71.83: 1210 71.83 - 107.74: 93 107.74 - 143.65: 12 143.65 - 179.57: 25 Dihedral angle restraints: 32548 sinusoidal: 24167 harmonic: 8381 Sorted by residual: dihedral pdb=" C5' G A1400 " pdb=" C4' G A1400 " pdb=" C3' G A1400 " pdb=" O3' G A1400 " ideal model delta sinusoidal sigma weight residual 147.00 81.95 65.05 1 8.00e+00 1.56e-02 8.67e+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 17.14 -177.14 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" C4' G A1400 " pdb=" C3' G A1400 " pdb=" C2' G A1400 " pdb=" C1' G A1400 " ideal model delta sinusoidal sigma weight residual -35.00 29.18 -64.18 1 8.00e+00 1.56e-02 8.47e+01 ... (remaining 32545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 7649 0.112 - 0.224: 2735 0.224 - 0.335: 567 0.335 - 0.447: 7 0.447 - 0.559: 2 Chirality restraints: 10960 Sorted by residual: 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 -2.19 -0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" C3' U A1484 " pdb=" C4' U A1484 " pdb=" O3' U A1484 " pdb=" C2' U A1484 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.46 2.00e-01 2.50e+01 5.40e+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 -2.31 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 10957 not shown) Planarity restraints: 5590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 116 " 0.000 2.00e-02 2.50e+03 2.00e-02 1.20e+01 pdb=" N9 G A 116 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G A 116 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G A 116 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 116 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G A 116 " -0.013 2.00e-02 2.50e+03 pdb=" O6 G A 116 " 0.025 2.00e-02 2.50e+03 pdb=" N1 G A 116 " -0.046 2.00e-02 2.50e+03 pdb=" C2 G A 116 " 0.042 2.00e-02 2.50e+03 pdb=" N2 G A 116 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 116 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 116 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 184 " -0.011 2.00e-02 2.50e+03 1.86e-02 1.03e+01 pdb=" N9 G A 184 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A 184 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 184 " 0.011 2.00e-02 2.50e+03 pdb=" C5 G A 184 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G A 184 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G A 184 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G A 184 " -0.043 2.00e-02 2.50e+03 pdb=" C2 G A 184 " 0.042 2.00e-02 2.50e+03 pdb=" N2 G A 184 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 184 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G A 184 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1272 " 0.003 2.00e-02 2.50e+03 1.82e-02 9.91e+00 pdb=" N9 G A1272 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G A1272 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A1272 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A1272 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A1272 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G A1272 " -0.024 2.00e-02 2.50e+03 pdb=" N1 G A1272 " 0.048 2.00e-02 2.50e+03 pdb=" C2 G A1272 " -0.029 2.00e-02 2.50e+03 pdb=" N2 G A1272 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A1272 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A1272 " -0.006 2.00e-02 2.50e+03 ... (remaining 5587 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 7513 2.77 - 3.30: 49550 3.30 - 3.83: 110884 3.83 - 4.37: 132324 4.37 - 4.90: 186409 Nonbonded interactions: 486680 Sorted by model distance: nonbonded pdb=" O ASN M 40 " pdb=" OG1 THR M 43 " model vdw 2.232 2.440 nonbonded pdb=" OP1 G A1204 " pdb=" O2' C A1303 " model vdw 2.245 2.440 nonbonded pdb=" N4 C A1145 " pdb=" O6 G A1156 " model vdw 2.250 2.520 nonbonded pdb=" O2' G A 434 " pdb=" O4 U A 479 " model vdw 2.261 2.440 nonbonded pdb=" O2' C A 208 " pdb=" O4' U A 209 " model vdw 2.268 2.440 ... (remaining 486675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'U' and resid 32 through 290) selection = (chain 'W' and resid 32 through 290) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 10.680 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 147.520 Find NCS groups from input model: 1.280 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 0.041 59402 Z= 0.493 Angle : 1.155 11.439 87573 Z= 0.733 Chirality : 0.106 0.559 10960 Planarity : 0.004 0.021 5590 Dihedral : 16.391 179.568 27148 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.46 % Favored : 93.23 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.11 % 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: -0.70 (0.15), residues: 2865 helix: 0.61 (0.15), residues: 1122 sheet: 0.18 (0.25), residues: 459 loop : -1.71 (0.16), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 429 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 435 average time/residue: 0.6101 time to fit residues: 426.4444 Evaluate side-chains 337 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 time to evaluate : 2.961 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3962 time to fit residues: 4.1219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 336 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 204 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 389 optimal weight: 8.9990 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 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN C 63 ASN C 98 ASN D 160 GLN M 77 ASN O 71 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 265 ASN ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 242 ASN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 59402 Z= 0.294 Angle : 0.624 10.730 87573 Z= 0.315 Chirality : 0.038 0.255 10960 Planarity : 0.005 0.043 5590 Dihedral : 15.816 179.729 21128 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer Outliers : 1.67 % 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: 2865 helix: 0.90 (0.15), residues: 1161 sheet: 0.18 (0.25), residues: 465 loop : -1.52 (0.17), residues: 1239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 338 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 363 average time/residue: 0.5840 time to fit residues: 347.7426 Evaluate side-chains 327 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 304 time to evaluate : 3.055 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4008 time to fit residues: 21.1896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 324 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 421 optimal weight: 0.9990 chunk 347 optimal weight: 1.9990 chunk 387 optimal weight: 30.0000 chunk 133 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 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 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN D 160 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS W 242 ASN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 59402 Z= 0.256 Angle : 0.593 10.510 87573 Z= 0.300 Chirality : 0.037 0.259 10960 Planarity : 0.004 0.040 5590 Dihedral : 15.815 179.579 21128 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.28 % Favored : 93.61 % Rotamer Outliers : 1.38 % 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: -0.28 (0.16), residues: 2865 helix: 1.02 (0.15), residues: 1148 sheet: 0.17 (0.25), residues: 464 loop : -1.48 (0.17), residues: 1253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 333 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 12 residues processed: 357 average time/residue: 0.5684 time to fit residues: 336.6695 Evaluate side-chains 318 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 306 time to evaluate : 3.000 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3921 time to fit residues: 12.3374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 202 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 391 optimal weight: 20.0000 chunk 414 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 242 ASN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 59402 Z= 0.331 Angle : 0.639 10.976 87573 Z= 0.322 Chirality : 0.039 0.275 10960 Planarity : 0.005 0.041 5590 Dihedral : 15.925 179.487 21128 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.64 % Rotamer Outliers : 2.20 % 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: -0.41 (0.16), residues: 2865 helix: 0.89 (0.15), residues: 1149 sheet: 0.03 (0.25), residues: 462 loop : -1.49 (0.17), residues: 1254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 319 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 34 residues processed: 355 average time/residue: 0.5732 time to fit residues: 336.2826 Evaluate side-chains 340 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 306 time to evaluate : 3.105 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3965 time to fit residues: 29.1804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 353 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 372 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 98 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** U 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 ASN ** W 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 59402 Z= 0.373 Angle : 0.680 11.390 87573 Z= 0.342 Chirality : 0.041 0.290 10960 Planarity : 0.005 0.048 5590 Dihedral : 16.064 179.842 21128 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.43 % Rotamer Outliers : 2.20 % 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: -0.63 (0.16), residues: 2865 helix: 0.71 (0.15), residues: 1154 sheet: -0.23 (0.25), residues: 466 loop : -1.58 (0.17), residues: 1245 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 320 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 29 residues processed: 357 average time/residue: 0.5628 time to fit residues: 333.2335 Evaluate side-chains 334 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 305 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4025 time to fit residues: 25.4353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 20.0000 chunk 373 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 415 optimal weight: 6.9990 chunk 344 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 chunk 217 optimal weight: 0.0770 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS C 63 ASN C 108 ASN E 65 ASN O 28 GLN U 43 HIS U 242 ASN ** W 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 59402 Z= 0.209 Angle : 0.580 10.717 87573 Z= 0.295 Chirality : 0.036 0.240 10960 Planarity : 0.004 0.044 5590 Dihedral : 15.868 179.934 21128 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.96 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2865 helix: 1.02 (0.16), residues: 1142 sheet: -0.11 (0.25), residues: 469 loop : -1.40 (0.18), residues: 1254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 327 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 343 average time/residue: 0.5813 time to fit residues: 329.3761 Evaluate side-chains 314 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 304 time to evaluate : 3.015 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4075 time to fit residues: 11.1478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 349 optimal weight: 0.5980 chunk 231 optimal weight: 10.0000 chunk 413 optimal weight: 8.9990 chunk 258 optimal weight: 0.4980 chunk 252 optimal weight: 3.9990 chunk 190 optimal weight: 0.4980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS C 63 ASN C 98 ASN O 28 GLN S 65 ASN U 43 HIS ** W 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 242 ASN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 59402 Z= 0.182 Angle : 0.558 10.396 87573 Z= 0.283 Chirality : 0.035 0.245 10960 Planarity : 0.004 0.041 5590 Dihedral : 15.738 179.549 21128 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.79 % Favored : 94.14 % Rotamer Outliers : 0.69 % 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 (0.16), residues: 2865 helix: 1.15 (0.16), residues: 1141 sheet: -0.04 (0.25), residues: 479 loop : -1.33 (0.18), residues: 1245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 326 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 333 average time/residue: 0.5863 time to fit residues: 321.4511 Evaluate side-chains 318 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 309 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4027 time to fit residues: 10.3354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 246 optimal weight: 0.4980 chunk 124 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS C 63 ASN O 28 GLN S 65 ASN ** W 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 253 GLN ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 59402 Z= 0.246 Angle : 0.587 10.227 87573 Z= 0.298 Chirality : 0.036 0.253 10960 Planarity : 0.004 0.041 5590 Dihedral : 15.777 179.904 21128 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.53 % Favored : 93.44 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2865 helix: 1.02 (0.16), residues: 1150 sheet: -0.07 (0.25), residues: 468 loop : -1.33 (0.18), residues: 1247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 314 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 324 average time/residue: 0.6348 time to fit residues: 340.0947 Evaluate side-chains 324 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 306 time to evaluate : 3.010 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4171 time to fit residues: 17.8600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 361 optimal weight: 4.9990 chunk 385 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 348 optimal weight: 0.8980 chunk 364 optimal weight: 9.9990 chunk 383 optimal weight: 0.0020 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS O 28 GLN S 65 ASN ** W 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 59402 Z= 0.174 Angle : 0.563 10.314 87573 Z= 0.287 Chirality : 0.035 0.244 10960 Planarity : 0.004 0.056 5590 Dihedral : 15.755 179.658 21128 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.03 % Rotamer Outliers : 0.33 % 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 (0.16), residues: 2865 helix: 1.07 (0.16), residues: 1147 sheet: -0.06 (0.25), residues: 479 loop : -1.30 (0.18), residues: 1239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 311 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 317 average time/residue: 0.5900 time to fit residues: 307.8197 Evaluate side-chains 306 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 3.030 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3886 time to fit residues: 6.4447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 2.9990 chunk 407 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 427 optimal weight: 20.0000 chunk 393 optimal weight: 6.9990 chunk 340 optimal weight: 0.0980 chunk 35 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS B 212 GLN O 28 GLN S 65 ASN T 90 GLN U 43 HIS ** W 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 59402 Z= 0.167 Angle : 0.545 9.887 87573 Z= 0.278 Chirality : 0.034 0.229 10960 Planarity : 0.004 0.049 5590 Dihedral : 15.659 179.247 21128 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.38 % Rotamer Outliers : 0.37 % 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 (0.16), residues: 2865 helix: 1.18 (0.16), residues: 1143 sheet: 0.02 (0.25), residues: 479 loop : -1.27 (0.18), residues: 1243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5730 Ramachandran restraints generated. 2865 Oldfield, 0 Emsley, 2865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 321 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 323 average time/residue: 0.5893 time to fit residues: 313.0969 Evaluate side-chains 314 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 307 time to evaluate : 2.977 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3989 time to fit residues: 8.7606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.9990 chunk 362 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 313 optimal weight: 0.0370 chunk 50 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 350 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS B 212 GLN S 65 ASN U 43 HIS ** W 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053113 restraints weight = 190314.219| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.23 r_work: 0.2800 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 59402 Z= 0.313 Angle : 0.632 10.144 87573 Z= 0.318 Chirality : 0.038 0.269 10960 Planarity : 0.005 0.046 5590 Dihedral : 15.825 179.850 21128 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.95 % Favored : 93.02 % 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: -0.32 (0.16), residues: 2865 helix: 0.90 (0.15), residues: 1156 sheet: -0.11 (0.25), residues: 468 loop : -1.32 (0.18), residues: 1241 =============================================================================== Job complete usr+sys time: 8027.16 seconds wall clock time: 144 minutes 41.94 seconds (8681.94 seconds total)