Starting phenix.real_space_refine on Wed Jan 17 23:38:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/01_2024/7v2m_31656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/01_2024/7v2m_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_31656/01_2024/7v2m_31656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/01_2024/7v2m_31656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/01_2024/7v2m_31656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2m_31656/01_2024/7v2m_31656.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 21.97, per 1000 atoms: 0.40 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: 21.54 Conformation dependent library (CDL) restraints added in 3.4 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: 19.18 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: 44.75 Time building geometry restraints manager: 23.32 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: 33478 35.91 - 71.83: 3431 71.83 - 107.74: 506 107.74 - 143.65: 12 143.65 - 179.57: 25 Dihedral angle restraints: 37452 sinusoidal: 29071 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 37449 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: 1.320 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: 0.040 Extract box with map and model: 9.440 Check model and map are aligned: 0.620 Set scattering table: 0.410 Process input model: 159.170 Find NCS groups from input model: 1.140 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.620 ------------------------------------------------------------------------------- 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 : 23.100 179.568 32052 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 % Allowed : 4.64 % Favored : 95.03 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 156 HIS 0.006 0.002 HIS G 153 PHE 0.015 0.002 PHE D 79 TYR 0.018 0.002 TYR H 65 ARG 0.007 0.001 ARG S 3 *********************** 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 : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 GLN cc_start: 0.7621 (mt0) cc_final: 0.7368 (mt0) REVERT: D 33 MET cc_start: 0.8741 (mmm) cc_final: 0.8509 (mmp) REVERT: E 66 MET cc_start: 0.8569 (mmt) cc_final: 0.8319 (mmt) REVERT: G 45 ASP cc_start: 0.7472 (m-30) cc_final: 0.7266 (m-30) REVERT: G 86 GLN cc_start: 0.7678 (mp10) cc_final: 0.7369 (mp10) REVERT: G 144 MET cc_start: 0.8650 (tpp) cc_final: 0.8034 (tpp) REVERT: K 75 TYR cc_start: 0.6948 (m-80) cc_final: 0.6672 (m-80) REVERT: K 111 ASP cc_start: 0.7599 (t0) cc_final: 0.7383 (t0) REVERT: K 124 LYS cc_start: 0.7398 (mmmt) cc_final: 0.7180 (mmmt) REVERT: M 50 GLU cc_start: 0.6471 (mm-30) cc_final: 0.6107 (tp30) REVERT: M 66 LEU cc_start: 0.7489 (mm) cc_final: 0.7277 (mm) REVERT: M 70 LEU cc_start: 0.7714 (mt) cc_final: 0.7369 (mt) REVERT: M 87 TYR cc_start: 0.7173 (t80) cc_final: 0.6926 (t80) REVERT: N 8 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7931 (mm-30) REVERT: N 17 LYS cc_start: 0.8791 (tppt) cc_final: 0.8355 (tptt) REVERT: O 84 LYS cc_start: 0.8477 (mtmm) cc_final: 0.7942 (mtmm) REVERT: R 36 ASN cc_start: 0.8430 (t0) cc_final: 0.7657 (t0) REVERT: S 25 LYS cc_start: 0.8292 (tttt) cc_final: 0.8019 (tmmt) REVERT: T 42 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8202 (tm-30) REVERT: T 46 GLU cc_start: 0.8540 (tp30) cc_final: 0.7702 (tm-30) REVERT: U 18 TYR cc_start: 0.4317 (m-80) cc_final: 0.3985 (m-10) REVERT: U 43 HIS cc_start: 0.4902 (m90) cc_final: 0.4553 (m-70) REVERT: U 105 LYS cc_start: 0.5476 (tptt) cc_final: 0.5237 (pttp) REVERT: U 131 TYR cc_start: 0.5904 (p90) cc_final: 0.5435 (p90) REVERT: U 171 TYR cc_start: 0.7530 (t80) cc_final: 0.7280 (t80) REVERT: U 188 MET cc_start: 0.6954 (ttt) cc_final: 0.6242 (ttp) REVERT: V 5 ASP cc_start: 0.6703 (t0) cc_final: 0.6276 (t0) REVERT: W 251 LYS cc_start: 0.5313 (tttt) cc_final: 0.5067 (tmtt) outliers start: 8 outliers final: 1 residues processed: 435 average time/residue: 0.5903 time to fit residues: 413.6878 Evaluate side-chains 343 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 267 ASP 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: 7.9990 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 D 160 GLN M 77 ASN O 71 GLN R 36 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 59402 Z= 0.283 Angle : 0.615 10.500 87573 Z= 0.311 Chirality : 0.038 0.266 10960 Planarity : 0.004 0.044 5590 Dihedral : 23.786 179.653 26034 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer: Outliers : 1.43 % Allowed : 10.63 % Favored : 87.94 % 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: -0.33 (0.16), residues: 2865 helix: 0.93 (0.15), residues: 1155 sheet: 0.21 (0.25), residues: 459 loop : -1.51 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 167 HIS 0.008 0.001 HIS S 14 PHE 0.024 0.002 PHE G 62 TYR 0.017 0.002 TYR I 88 ARG 0.004 0.001 ARG W 161 *********************** 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 377 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 342 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 GLN cc_start: 0.7523 (pt0) cc_final: 0.7138 (pm20) REVERT: B 90 MET cc_start: 0.8011 (mmt) cc_final: 0.7705 (mmt) REVERT: D 33 MET cc_start: 0.8789 (mmm) cc_final: 0.8483 (mmp) REVERT: F 18 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7912 (mm-40) REVERT: F 70 ASP cc_start: 0.8177 (p0) cc_final: 0.7964 (p0) REVERT: G 42 ILE cc_start: 0.7420 (tp) cc_final: 0.7122 (tp) REVERT: G 45 ASP cc_start: 0.7591 (m-30) cc_final: 0.7327 (m-30) REVERT: G 78 ARG cc_start: 0.4956 (OUTLIER) cc_final: 0.4749 (tpp-160) REVERT: I 34 ASN cc_start: 0.8791 (m-40) cc_final: 0.8384 (m110) REVERT: K 54 ARG cc_start: 0.7350 (ptm160) cc_final: 0.7108 (ptm-80) REVERT: K 75 TYR cc_start: 0.7110 (m-80) cc_final: 0.6733 (m-80) REVERT: K 111 ASP cc_start: 0.7725 (t0) cc_final: 0.7406 (t0) REVERT: K 122 LYS cc_start: 0.7589 (mmmm) cc_final: 0.7334 (mmtt) REVERT: K 124 LYS cc_start: 0.7403 (mmmt) cc_final: 0.7169 (mmmt) REVERT: M 70 LEU cc_start: 0.7713 (mt) cc_final: 0.7408 (mt) REVERT: M 86 CYS cc_start: 0.7650 (t) cc_final: 0.7112 (t) REVERT: O 5 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8067 (ttmt) REVERT: O 7 GLU cc_start: 0.8200 (pm20) cc_final: 0.7938 (pm20) REVERT: R 36 ASN cc_start: 0.8350 (t0) cc_final: 0.7665 (t0) REVERT: R 42 ARG cc_start: 0.7650 (mmt-90) cc_final: 0.7354 (mmt-90) REVERT: S 25 LYS cc_start: 0.8294 (tttt) cc_final: 0.7983 (tmmt) REVERT: S 71 LEU cc_start: 0.8890 (mp) cc_final: 0.8560 (mt) REVERT: T 56 MET cc_start: 0.8121 (tmm) cc_final: 0.7721 (tmm) REVERT: U 43 HIS cc_start: 0.4455 (m90) cc_final: 0.4241 (m-70) REVERT: U 105 LYS cc_start: 0.5354 (tptt) cc_final: 0.5117 (pttp) REVERT: U 131 TYR cc_start: 0.5928 (p90) cc_final: 0.5317 (p90) REVERT: U 171 TYR cc_start: 0.7430 (t80) cc_final: 0.7205 (t80) REVERT: V 5 ASP cc_start: 0.6961 (t0) cc_final: 0.6502 (t0) REVERT: V 10 ARG cc_start: 0.8339 (tpp80) cc_final: 0.8084 (tpp80) outliers start: 35 outliers final: 22 residues processed: 365 average time/residue: 0.5731 time to fit residues: 342.9694 Evaluate side-chains 337 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 314 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 390 optimal weight: 8.9990 chunk 421 optimal weight: 9.9990 chunk 347 optimal weight: 3.9990 chunk 387 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 313 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 ** 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: 0.8463 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 59402 Z= 0.256 Angle : 0.591 10.572 87573 Z= 0.300 Chirality : 0.037 0.260 10960 Planarity : 0.004 0.040 5590 Dihedral : 23.755 179.738 26034 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.37 % Rotamer: Outliers : 2.16 % Allowed : 13.44 % Favored : 84.40 % 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: -0.27 (0.16), residues: 2865 helix: 1.01 (0.15), residues: 1154 sheet: 0.18 (0.25), residues: 460 loop : -1.47 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 167 HIS 0.009 0.001 HIS S 14 PHE 0.017 0.002 PHE O 15 TYR 0.018 0.002 TYR I 88 ARG 0.009 0.001 ARG K 18 *********************** 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 390 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 337 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 GLN cc_start: 0.7438 (pt0) cc_final: 0.7028 (pm20) REVERT: B 212 GLN cc_start: 0.7449 (mt0) cc_final: 0.7152 (mt0) REVERT: D 33 MET cc_start: 0.8718 (mmm) cc_final: 0.8491 (mmp) REVERT: E 9 LYS cc_start: 0.8797 (tppt) cc_final: 0.8489 (tppp) REVERT: F 18 GLN cc_start: 0.8233 (mm-40) cc_final: 0.8018 (mm-40) REVERT: F 70 ASP cc_start: 0.8199 (p0) cc_final: 0.7990 (p0) REVERT: G 42 ILE cc_start: 0.7445 (tp) cc_final: 0.7144 (tp) REVERT: G 45 ASP cc_start: 0.7473 (m-30) cc_final: 0.7189 (m-30) REVERT: I 34 ASN cc_start: 0.8960 (m-40) cc_final: 0.8691 (m110) REVERT: K 54 ARG cc_start: 0.7333 (ptm160) cc_final: 0.7037 (ptm-80) REVERT: K 63 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6978 (tt) REVERT: K 75 TYR cc_start: 0.7007 (m-80) cc_final: 0.6692 (m-80) REVERT: K 111 ASP cc_start: 0.7669 (t0) cc_final: 0.7203 (t70) REVERT: K 122 LYS cc_start: 0.7200 (mmmm) cc_final: 0.6977 (mmtt) REVERT: M 31 LYS cc_start: 0.8195 (tmmt) cc_final: 0.7901 (tptt) REVERT: M 70 LEU cc_start: 0.7707 (mt) cc_final: 0.7359 (mt) REVERT: N 61 TRP cc_start: 0.7624 (p90) cc_final: 0.7229 (p90) REVERT: O 5 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8063 (ttmt) REVERT: R 36 ASN cc_start: 0.8421 (t0) cc_final: 0.7381 (t0) REVERT: S 14 HIS cc_start: 0.7986 (p-80) cc_final: 0.7523 (p90) REVERT: S 25 LYS cc_start: 0.8275 (tttt) cc_final: 0.7911 (tmmt) REVERT: S 71 LEU cc_start: 0.8884 (mp) cc_final: 0.8549 (mt) REVERT: T 56 MET cc_start: 0.8125 (tmm) cc_final: 0.7773 (tmm) REVERT: U 43 HIS cc_start: 0.4206 (m90) cc_final: 0.3812 (m-70) REVERT: U 131 TYR cc_start: 0.6487 (p90) cc_final: 0.5839 (p90) REVERT: U 171 TYR cc_start: 0.7452 (t80) cc_final: 0.7220 (t80) REVERT: U 188 MET cc_start: 0.6634 (ttm) cc_final: 0.5988 (ttp) REVERT: V 5 ASP cc_start: 0.7021 (t0) cc_final: 0.6556 (t0) REVERT: W 271 ARG cc_start: 0.6600 (tpp-160) cc_final: 0.6330 (tpp-160) outliers start: 53 outliers final: 32 residues processed: 370 average time/residue: 0.5504 time to fit residues: 337.2037 Evaluate side-chains 349 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 316 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain M residue 64 TRP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 120 ASP Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain W residue 278 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 391 optimal weight: 20.0000 chunk 414 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 371 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 D 160 GLN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN U 241 ASN U 242 ASN 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: 0.8491 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 59402 Z= 0.365 Angle : 0.669 11.025 87573 Z= 0.336 Chirality : 0.040 0.289 10960 Planarity : 0.005 0.043 5590 Dihedral : 23.811 179.326 26032 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.64 % Rotamer: Outliers : 3.30 % Allowed : 15.76 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2865 helix: 0.79 (0.15), residues: 1154 sheet: -0.06 (0.25), residues: 465 loop : -1.55 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 167 HIS 0.007 0.002 HIS M 92 PHE 0.019 0.002 PHE W 180 TYR 0.019 0.002 TYR I 88 ARG 0.006 0.001 ARG P 8 *********************** 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 413 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 332 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: C 165 THR cc_start: 0.8866 (m) cc_final: 0.8533 (p) REVERT: D 33 MET cc_start: 0.8735 (mmm) cc_final: 0.8197 (mmp) REVERT: F 18 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7771 (mm-40) REVERT: F 70 ASP cc_start: 0.8204 (p0) cc_final: 0.7979 (p0) REVERT: G 42 ILE cc_start: 0.7547 (tp) cc_final: 0.7249 (tp) REVERT: G 45 ASP cc_start: 0.7423 (m-30) cc_final: 0.7141 (m-30) REVERT: I 31 GLN cc_start: 0.6417 (tm-30) cc_final: 0.5960 (tm-30) REVERT: I 51 ARG cc_start: 0.8138 (ptp-110) cc_final: 0.7859 (ttp80) REVERT: K 54 ARG cc_start: 0.7322 (ptm160) cc_final: 0.7075 (ptm-80) REVERT: K 75 TYR cc_start: 0.7084 (m-80) cc_final: 0.6798 (m-80) REVERT: K 111 ASP cc_start: 0.7732 (t0) cc_final: 0.7194 (t70) REVERT: M 70 LEU cc_start: 0.7552 (mt) cc_final: 0.7203 (mt) REVERT: M 83 ASP cc_start: 0.6786 (m-30) cc_final: 0.6510 (m-30) REVERT: R 36 ASN cc_start: 0.8428 (t0) cc_final: 0.7350 (t0) REVERT: S 25 LYS cc_start: 0.8371 (tttt) cc_final: 0.7968 (tmmt) REVERT: S 71 LEU cc_start: 0.8911 (mp) cc_final: 0.8565 (mt) REVERT: T 56 MET cc_start: 0.7915 (tmm) cc_final: 0.7522 (tmm) REVERT: U 43 HIS cc_start: 0.4305 (m90) cc_final: 0.3825 (m-70) REVERT: U 131 TYR cc_start: 0.6453 (p90) cc_final: 0.5810 (p90) REVERT: U 171 TYR cc_start: 0.7393 (t80) cc_final: 0.7182 (t80) REVERT: U 188 MET cc_start: 0.6681 (ttm) cc_final: 0.6006 (ttp) REVERT: V 5 ASP cc_start: 0.7086 (t0) cc_final: 0.6615 (t0) REVERT: W 271 ARG cc_start: 0.6678 (tpp-160) cc_final: 0.6340 (tpp-160) outliers start: 81 outliers final: 56 residues processed: 389 average time/residue: 0.5480 time to fit residues: 356.2071 Evaluate side-chains 377 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 320 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 TRP Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 120 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain W residue 152 VAL Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 223 PHE Chi-restraints excluded: chain W residue 278 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 286 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 372 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS C 108 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1460 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= 0.230 Angle : 0.586 10.868 87573 Z= 0.296 Chirality : 0.036 0.251 10960 Planarity : 0.004 0.043 5590 Dihedral : 23.755 179.708 26032 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.14 % Rotamer: Outliers : 3.18 % Allowed : 17.43 % Favored : 79.39 % 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: -0.33 (0.16), residues: 2865 helix: 1.00 (0.15), residues: 1148 sheet: -0.06 (0.25), residues: 470 loop : -1.44 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 167 HIS 0.007 0.001 HIS S 14 PHE 0.013 0.001 PHE W 180 TYR 0.017 0.001 TYR I 88 ARG 0.003 0.000 ARG C 140 *********************** 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 413 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 335 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 GLN cc_start: 0.7357 (mt0) cc_final: 0.7114 (mt0) REVERT: C 165 THR cc_start: 0.8853 (m) cc_final: 0.8598 (p) REVERT: D 33 MET cc_start: 0.8680 (mmm) cc_final: 0.8190 (mmp) REVERT: F 18 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7778 (mm110) REVERT: F 70 ASP cc_start: 0.8181 (p0) cc_final: 0.7950 (p0) REVERT: G 42 ILE cc_start: 0.7433 (tp) cc_final: 0.7125 (tp) REVERT: G 45 ASP cc_start: 0.7421 (m-30) cc_final: 0.7150 (m-30) REVERT: I 31 GLN cc_start: 0.6497 (tm-30) cc_final: 0.6106 (tm-30) REVERT: I 51 ARG cc_start: 0.8055 (ptp-110) cc_final: 0.7783 (ttp80) REVERT: K 54 ARG cc_start: 0.7312 (ptm160) cc_final: 0.7045 (ptm-80) REVERT: K 75 TYR cc_start: 0.7081 (m-80) cc_final: 0.6873 (m-80) REVERT: K 111 ASP cc_start: 0.7758 (t0) cc_final: 0.7231 (t70) REVERT: K 124 LYS cc_start: 0.7430 (pttm) cc_final: 0.7004 (mmmt) REVERT: M 31 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7978 (tptt) REVERT: M 70 LEU cc_start: 0.7603 (mt) cc_final: 0.7236 (mt) REVERT: M 83 ASP cc_start: 0.6693 (m-30) cc_final: 0.6414 (m-30) REVERT: R 36 ASN cc_start: 0.8395 (t0) cc_final: 0.7312 (t0) REVERT: S 25 LYS cc_start: 0.8370 (tttt) cc_final: 0.7953 (tmmt) REVERT: S 71 LEU cc_start: 0.8823 (mp) cc_final: 0.8460 (mt) REVERT: T 56 MET cc_start: 0.7873 (tmm) cc_final: 0.7439 (tmm) REVERT: U 36 ILE cc_start: 0.5296 (mm) cc_final: 0.4937 (mm) REVERT: U 43 HIS cc_start: 0.4493 (m90) cc_final: 0.4049 (m-70) REVERT: U 83 LEU cc_start: 0.4160 (mt) cc_final: 0.3839 (mm) REVERT: U 131 TYR cc_start: 0.6623 (p90) cc_final: 0.6021 (p90) REVERT: U 188 MET cc_start: 0.6687 (ttm) cc_final: 0.5994 (ttp) REVERT: V 5 ASP cc_start: 0.7029 (t0) cc_final: 0.6560 (t0) outliers start: 78 outliers final: 55 residues processed: 388 average time/residue: 0.5578 time to fit residues: 361.5607 Evaluate side-chains 377 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 322 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 TRP Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 15 MET Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 120 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain W residue 152 VAL Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 223 PHE Chi-restraints excluded: chain W residue 278 GLU 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: 4.9990 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: 0.1980 chunk 192 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 chunk 217 optimal weight: 0.0040 overall best weight: 3.0398 ------------------------------------------------------------------------------- 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 113 HIS C 63 ASN C 98 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 59402 Z= 0.203 Angle : 0.563 10.480 87573 Z= 0.285 Chirality : 0.035 0.241 10960 Planarity : 0.004 0.044 5590 Dihedral : 23.704 179.974 26032 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 3.34 % Allowed : 18.13 % Favored : 78.53 % 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: -0.21 (0.16), residues: 2865 helix: 1.15 (0.16), residues: 1143 sheet: -0.08 (0.25), residues: 480 loop : -1.39 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 167 HIS 0.006 0.001 HIS S 14 PHE 0.014 0.001 PHE K 125 TYR 0.018 0.001 TYR I 88 ARG 0.002 0.000 ARG G 78 *********************** 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 422 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 340 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: C 165 THR cc_start: 0.8783 (m) cc_final: 0.8543 (p) REVERT: D 33 MET cc_start: 0.8648 (mmm) cc_final: 0.8128 (mmp) REVERT: D 160 GLN cc_start: 0.8797 (mt0) cc_final: 0.8174 (mp10) REVERT: F 18 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7737 (mm-40) REVERT: F 54 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7930 (mmtt) REVERT: F 70 ASP cc_start: 0.8186 (p0) cc_final: 0.7951 (p0) REVERT: G 42 ILE cc_start: 0.7572 (tp) cc_final: 0.6955 (tp) REVERT: G 45 ASP cc_start: 0.7419 (m-30) cc_final: 0.7141 (m-30) REVERT: G 85 TYR cc_start: 0.7349 (m-80) cc_final: 0.6670 (m-80) REVERT: I 31 GLN cc_start: 0.6565 (tm-30) cc_final: 0.6219 (tm-30) REVERT: I 51 ARG cc_start: 0.8070 (ptp-110) cc_final: 0.7804 (ttp80) REVERT: K 18 ARG cc_start: 0.5362 (mtm110) cc_final: 0.5040 (ptp90) REVERT: K 54 ARG cc_start: 0.7326 (ptm160) cc_final: 0.7045 (ptm-80) REVERT: K 75 TYR cc_start: 0.7016 (m-80) cc_final: 0.6743 (m-80) REVERT: K 111 ASP cc_start: 0.7764 (t0) cc_final: 0.7232 (t70) REVERT: K 124 LYS cc_start: 0.7450 (pttm) cc_final: 0.7050 (mmmt) REVERT: L 117 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: M 31 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7939 (tptt) REVERT: M 70 LEU cc_start: 0.7606 (mt) cc_final: 0.7236 (mt) REVERT: M 83 ASP cc_start: 0.6867 (m-30) cc_final: 0.6654 (m-30) REVERT: M 86 CYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6890 (t) REVERT: R 36 ASN cc_start: 0.8399 (t0) cc_final: 0.7356 (t0) REVERT: R 62 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8093 (mt-10) REVERT: S 25 LYS cc_start: 0.8325 (tttt) cc_final: 0.7884 (tmmt) REVERT: S 71 LEU cc_start: 0.8806 (mp) cc_final: 0.8440 (mt) REVERT: U 36 ILE cc_start: 0.5302 (mm) cc_final: 0.4940 (mm) REVERT: U 43 HIS cc_start: 0.4551 (m90) cc_final: 0.4125 (m-70) REVERT: U 131 TYR cc_start: 0.6591 (p90) cc_final: 0.6026 (p90) REVERT: U 188 MET cc_start: 0.6711 (ttm) cc_final: 0.5974 (ttp) REVERT: V 5 ASP cc_start: 0.6988 (t0) cc_final: 0.6531 (t0) outliers start: 82 outliers final: 60 residues processed: 399 average time/residue: 0.5613 time to fit residues: 372.5405 Evaluate side-chains 387 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 324 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 TRP Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 120 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain W residue 152 VAL Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 223 PHE Chi-restraints excluded: chain W residue 278 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 236 optimal weight: 0.0030 chunk 303 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 413 optimal weight: 0.0570 chunk 258 optimal weight: 0.5980 chunk 252 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.5312 ------------------------------------------------------------------------------- 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 113 HIS C 63 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN T 90 GLN U 241 ASN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 59402 Z= 0.144 Angle : 0.526 9.891 87573 Z= 0.266 Chirality : 0.033 0.216 10960 Planarity : 0.004 0.042 5590 Dihedral : 23.602 179.578 26032 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 2.69 % Allowed : 19.39 % Favored : 77.92 % 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: 0.01 (0.16), residues: 2865 helix: 1.36 (0.16), residues: 1141 sheet: 0.06 (0.25), residues: 479 loop : -1.32 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 167 HIS 0.005 0.001 HIS S 14 PHE 0.011 0.001 PHE I 33 TYR 0.019 0.001 TYR I 88 ARG 0.003 0.000 ARG W 81 *********************** 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 410 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 344 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7969 (pt) REVERT: B 94 ASN cc_start: 0.8973 (p0) cc_final: 0.8493 (p0) REVERT: B 205 ASP cc_start: 0.6327 (p0) cc_final: 0.5761 (p0) REVERT: C 165 THR cc_start: 0.8650 (m) cc_final: 0.8382 (p) REVERT: D 33 MET cc_start: 0.8589 (mmm) cc_final: 0.8072 (mmp) REVERT: E 9 LYS cc_start: 0.8793 (tppt) cc_final: 0.8438 (tppp) REVERT: E 10 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8234 (tmm) REVERT: F 27 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8298 (tp-100) REVERT: F 70 ASP cc_start: 0.8367 (p0) cc_final: 0.8123 (p0) REVERT: G 42 ILE cc_start: 0.7536 (tp) cc_final: 0.6902 (tp) REVERT: G 45 ASP cc_start: 0.7342 (m-30) cc_final: 0.7047 (m-30) REVERT: G 85 TYR cc_start: 0.7313 (m-80) cc_final: 0.6674 (m-80) REVERT: I 31 GLN cc_start: 0.6753 (tm-30) cc_final: 0.6468 (tm-30) REVERT: I 51 ARG cc_start: 0.8129 (ptp-110) cc_final: 0.7809 (ttp80) REVERT: I 127 LYS cc_start: 0.7818 (tmtt) cc_final: 0.7571 (tppt) REVERT: J 95 GLU cc_start: 0.7735 (pp20) cc_final: 0.7474 (pp20) REVERT: K 18 ARG cc_start: 0.5496 (mtm110) cc_final: 0.5207 (ptp90) REVERT: K 54 ARG cc_start: 0.7425 (ptm160) cc_final: 0.7127 (ptm-80) REVERT: K 63 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7381 (tt) REVERT: K 75 TYR cc_start: 0.6957 (m-80) cc_final: 0.6698 (m-80) REVERT: K 111 ASP cc_start: 0.7756 (t0) cc_final: 0.7247 (t70) REVERT: K 124 LYS cc_start: 0.7561 (pttm) cc_final: 0.6930 (mmmt) REVERT: L 117 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: M 12 ASN cc_start: 0.7784 (p0) cc_final: 0.7485 (p0) REVERT: M 31 LYS cc_start: 0.8158 (tmmt) cc_final: 0.7911 (tptt) REVERT: M 36 LYS cc_start: 0.6902 (tmtt) cc_final: 0.6594 (ttpp) REVERT: M 70 LEU cc_start: 0.7635 (mt) cc_final: 0.7255 (mt) REVERT: M 86 CYS cc_start: 0.7362 (t) cc_final: 0.6941 (t) REVERT: N 61 TRP cc_start: 0.7591 (p90) cc_final: 0.7318 (p90) REVERT: R 36 ASN cc_start: 0.8423 (t0) cc_final: 0.7459 (t0) REVERT: S 25 LYS cc_start: 0.8365 (tttt) cc_final: 0.7928 (tmmt) REVERT: S 71 LEU cc_start: 0.8847 (mp) cc_final: 0.8497 (mt) REVERT: U 36 ILE cc_start: 0.5282 (mm) cc_final: 0.4920 (mm) REVERT: U 43 HIS cc_start: 0.4240 (m90) cc_final: 0.3843 (m-70) REVERT: U 131 TYR cc_start: 0.6478 (p90) cc_final: 0.5966 (p90) REVERT: U 188 MET cc_start: 0.6680 (ttm) cc_final: 0.5880 (ttp) REVERT: V 5 ASP cc_start: 0.6955 (t0) cc_final: 0.6501 (t0) outliers start: 66 outliers final: 46 residues processed: 388 average time/residue: 0.5605 time to fit residues: 362.1580 Evaluate side-chains 380 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 330 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 223 PHE Chi-restraints excluded: chain W residue 278 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 325 optimal weight: 0.0980 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 113 HIS E 73 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN O 28 GLN T 90 GLN ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 59402 Z= 0.201 Angle : 0.552 9.713 87573 Z= 0.278 Chirality : 0.034 0.241 10960 Planarity : 0.004 0.040 5590 Dihedral : 23.595 179.859 26032 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 2.65 % Allowed : 19.88 % Favored : 77.47 % 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: -0.00 (0.16), residues: 2865 helix: 1.33 (0.16), residues: 1140 sheet: 0.07 (0.25), residues: 480 loop : -1.30 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 167 HIS 0.006 0.001 HIS S 14 PHE 0.011 0.001 PHE I 33 TYR 0.019 0.001 TYR I 88 ARG 0.004 0.000 ARG W 161 *********************** 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 395 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 330 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 MET cc_start: 0.8637 (mmm) cc_final: 0.8101 (mmp) REVERT: D 160 GLN cc_start: 0.8789 (mt0) cc_final: 0.8161 (mp10) REVERT: F 27 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8282 (tp-100) REVERT: F 70 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8078 (p0) REVERT: G 42 ILE cc_start: 0.7561 (tp) cc_final: 0.6935 (tp) REVERT: G 45 ASP cc_start: 0.7402 (m-30) cc_final: 0.7127 (m-30) REVERT: G 85 TYR cc_start: 0.7350 (m-80) cc_final: 0.6695 (m-80) REVERT: I 31 GLN cc_start: 0.6734 (tm-30) cc_final: 0.6516 (tm-30) REVERT: I 51 ARG cc_start: 0.8064 (ptp-110) cc_final: 0.7793 (ttp80) REVERT: J 95 GLU cc_start: 0.7724 (pp20) cc_final: 0.7449 (pp20) REVERT: K 18 ARG cc_start: 0.5545 (mtm110) cc_final: 0.5259 (ptp90) REVERT: K 54 ARG cc_start: 0.7423 (ptm160) cc_final: 0.7173 (ptm-80) REVERT: K 75 TYR cc_start: 0.6938 (m-80) cc_final: 0.6627 (m-80) REVERT: K 111 ASP cc_start: 0.7685 (t0) cc_final: 0.7129 (t70) REVERT: K 124 LYS cc_start: 0.7467 (pttm) cc_final: 0.6950 (mmmt) REVERT: L 117 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: M 12 ASN cc_start: 0.7807 (p0) cc_final: 0.7509 (p0) REVERT: M 31 LYS cc_start: 0.8172 (tmmt) cc_final: 0.7914 (tptt) REVERT: M 70 LEU cc_start: 0.7627 (mt) cc_final: 0.7275 (mt) REVERT: P 27 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8398 (ptmm) REVERT: R 36 ASN cc_start: 0.8421 (t0) cc_final: 0.7449 (t0) REVERT: S 25 LYS cc_start: 0.8371 (tttt) cc_final: 0.7933 (tmmt) REVERT: S 71 LEU cc_start: 0.8792 (mp) cc_final: 0.8432 (mt) REVERT: T 46 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8060 (mm-30) REVERT: U 36 ILE cc_start: 0.5297 (mm) cc_final: 0.4931 (mm) REVERT: U 43 HIS cc_start: 0.4268 (m90) cc_final: 0.3859 (m-70) REVERT: U 131 TYR cc_start: 0.6538 (p90) cc_final: 0.6045 (p90) REVERT: U 188 MET cc_start: 0.6675 (ttm) cc_final: 0.5892 (ttp) REVERT: V 5 ASP cc_start: 0.6986 (t0) cc_final: 0.6526 (t0) outliers start: 65 outliers final: 54 residues processed: 374 average time/residue: 0.5662 time to fit residues: 352.0011 Evaluate side-chains 378 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 321 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 223 PHE Chi-restraints excluded: chain W residue 287 LEU 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: 7.9990 chunk 385 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 302 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 348 optimal weight: 1.9990 chunk 364 optimal weight: 8.9990 chunk 383 optimal weight: 8.9990 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 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 113 HIS B 212 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN S 65 ASN T 90 GLN U 241 ASN U 242 ASN W 253 GLN ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1703 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= 0.282 Angle : 0.610 9.859 87573 Z= 0.307 Chirality : 0.037 0.266 10960 Planarity : 0.005 0.043 5590 Dihedral : 23.660 179.948 26032 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 3.22 % Allowed : 19.55 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2865 helix: 1.07 (0.16), residues: 1155 sheet: -0.05 (0.25), residues: 473 loop : -1.31 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 167 HIS 0.006 0.001 HIS S 14 PHE 0.014 0.001 PHE S 74 TYR 0.019 0.002 TYR I 88 ARG 0.005 0.000 ARG P 8 *********************** 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 395 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 316 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.7865 (mmm) cc_final: 0.7550 (mmm) REVERT: D 33 MET cc_start: 0.8710 (mmm) cc_final: 0.8198 (mmp) REVERT: D 160 GLN cc_start: 0.8786 (mt0) cc_final: 0.8159 (mp10) REVERT: F 54 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7607 (mmtt) REVERT: F 67 MET cc_start: 0.8401 (ttp) cc_final: 0.8114 (ttm) REVERT: F 70 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8134 (p0) REVERT: G 42 ILE cc_start: 0.7461 (tp) cc_final: 0.7143 (tp) REVERT: G 45 ASP cc_start: 0.7412 (m-30) cc_final: 0.7134 (m-30) REVERT: I 51 ARG cc_start: 0.8083 (ptp-110) cc_final: 0.7820 (ttp80) REVERT: I 127 LYS cc_start: 0.7876 (tmtt) cc_final: 0.7533 (tppt) REVERT: K 18 ARG cc_start: 0.5536 (mtm110) cc_final: 0.5181 (ptp90) REVERT: K 75 TYR cc_start: 0.6999 (m-80) cc_final: 0.6655 (m-80) REVERT: K 111 ASP cc_start: 0.7673 (t0) cc_final: 0.7115 (t70) REVERT: L 117 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: M 12 ASN cc_start: 0.7893 (p0) cc_final: 0.7596 (p0) REVERT: M 31 LYS cc_start: 0.8189 (tmmt) cc_final: 0.7919 (tptt) REVERT: M 70 LEU cc_start: 0.7627 (mt) cc_final: 0.7271 (mt) REVERT: P 27 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8469 (ptmm) REVERT: R 36 ASN cc_start: 0.8408 (t0) cc_final: 0.7283 (t0) REVERT: S 25 LYS cc_start: 0.8337 (tttt) cc_final: 0.7878 (tmmt) REVERT: S 71 LEU cc_start: 0.8791 (mp) cc_final: 0.8440 (mt) REVERT: U 32 ILE cc_start: 0.5649 (OUTLIER) cc_final: 0.5351 (pt) REVERT: U 36 ILE cc_start: 0.5327 (mm) cc_final: 0.5067 (mm) REVERT: U 43 HIS cc_start: 0.4545 (m90) cc_final: 0.4103 (m-70) REVERT: U 131 TYR cc_start: 0.6564 (p90) cc_final: 0.6084 (p90) REVERT: V 5 ASP cc_start: 0.6972 (t0) cc_final: 0.6519 (t0) outliers start: 79 outliers final: 63 residues processed: 370 average time/residue: 0.5577 time to fit residues: 342.2012 Evaluate side-chains 383 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 316 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 223 PHE Chi-restraints excluded: chain W residue 278 GLU Chi-restraints excluded: chain W residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 0.9990 chunk 407 optimal weight: 9.9990 chunk 248 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 283 optimal weight: 0.0060 chunk 427 optimal weight: 10.0000 chunk 393 optimal weight: 0.4980 chunk 340 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- 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 113 HIS E 73 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN T 90 GLN U 29 ASN U 241 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 59402 Z= 0.132 Angle : 0.534 9.665 87573 Z= 0.270 Chirality : 0.033 0.230 10960 Planarity : 0.004 0.049 5590 Dihedral : 23.571 179.724 26032 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 2.08 % Allowed : 20.73 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2865 helix: 1.36 (0.16), residues: 1140 sheet: 0.12 (0.25), residues: 480 loop : -1.28 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 167 HIS 0.004 0.001 HIS S 14 PHE 0.009 0.001 PHE W 180 TYR 0.023 0.001 TYR I 88 ARG 0.004 0.000 ARG T 86 ********************** 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 387 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 336 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 MET cc_start: 0.8620 (mmm) cc_final: 0.8124 (mmp) REVERT: D 160 GLN cc_start: 0.8752 (mt0) cc_final: 0.8127 (mp10) REVERT: F 27 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8295 (tp-100) REVERT: F 67 MET cc_start: 0.8286 (ttp) cc_final: 0.8012 (ttm) REVERT: F 70 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7986 (p0) REVERT: G 42 ILE cc_start: 0.7536 (tp) cc_final: 0.7097 (tp) REVERT: G 45 ASP cc_start: 0.7437 (m-30) cc_final: 0.7160 (m-30) REVERT: I 51 ARG cc_start: 0.8052 (ptp-110) cc_final: 0.7790 (ttp80) REVERT: J 95 GLU cc_start: 0.7706 (pp20) cc_final: 0.7445 (pp20) REVERT: K 18 ARG cc_start: 0.5757 (mtm110) cc_final: 0.5469 (ptp90) REVERT: K 54 ARG cc_start: 0.7403 (ptm160) cc_final: 0.7185 (ptm-80) REVERT: K 63 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7414 (tt) REVERT: K 71 LYS cc_start: 0.6501 (ptpt) cc_final: 0.6153 (ptpp) REVERT: K 75 TYR cc_start: 0.6984 (m-80) cc_final: 0.6618 (m-80) REVERT: K 111 ASP cc_start: 0.7687 (t0) cc_final: 0.7125 (t70) REVERT: K 124 LYS cc_start: 0.7470 (pttm) cc_final: 0.7043 (mmmt) REVERT: L 117 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: M 12 ASN cc_start: 0.7835 (p0) cc_final: 0.7547 (p0) REVERT: M 31 LYS cc_start: 0.8158 (tmmt) cc_final: 0.7913 (tptt) REVERT: M 70 LEU cc_start: 0.7635 (mt) cc_final: 0.7259 (mt) REVERT: N 61 TRP cc_start: 0.7569 (p90) cc_final: 0.7323 (p90) REVERT: P 27 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8376 (ptmm) REVERT: P 73 LEU cc_start: 0.8909 (mp) cc_final: 0.8706 (mp) REVERT: R 36 ASN cc_start: 0.8413 (t0) cc_final: 0.7424 (t0) REVERT: S 25 LYS cc_start: 0.8436 (tttt) cc_final: 0.7949 (tmmt) REVERT: S 71 LEU cc_start: 0.8789 (mp) cc_final: 0.8429 (mt) REVERT: U 43 HIS cc_start: 0.4290 (m90) cc_final: 0.3935 (m-70) REVERT: U 131 TYR cc_start: 0.6562 (p90) cc_final: 0.6105 (p90) REVERT: U 188 MET cc_start: 0.6842 (ttt) cc_final: 0.6485 (ttt) REVERT: U 226 GLN cc_start: 0.7993 (mt0) cc_final: 0.7738 (tp40) REVERT: V 5 ASP cc_start: 0.6945 (t0) cc_final: 0.6484 (t0) outliers start: 51 outliers final: 38 residues processed: 372 average time/residue: 0.5630 time to fit residues: 345.8363 Evaluate side-chains 360 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 318 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain W residue 188 MET Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 223 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 7.9990 chunk 362 optimal weight: 0.0040 chunk 104 optimal weight: 10.0000 chunk 313 optimal weight: 0.0050 chunk 50 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 350 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 overall best weight: 5.4014 ------------------------------------------------------------------------------- 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 E 73 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN T 90 GLN U 241 ASN ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.053133 restraints weight = 190402.227| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.24 r_work: 0.2799 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 59402 Z= 0.325 Angle : 0.639 9.887 87573 Z= 0.320 Chirality : 0.038 0.274 10960 Planarity : 0.005 0.047 5590 Dihedral : 23.633 179.918 26032 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.70 % Favored : 93.26 % Rotamer: Outliers : 2.40 % Allowed : 20.69 % Favored : 76.90 % 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 (0.16), residues: 2865 helix: 1.00 (0.15), residues: 1154 sheet: -0.02 (0.25), residues: 471 loop : -1.30 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 167 HIS 0.006 0.001 HIS M 92 PHE 0.014 0.002 PHE S 74 TYR 0.022 0.002 TYR U 171 ARG 0.006 0.001 ARG P 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8770.14 seconds wall clock time: 157 minutes 31.49 seconds (9451.49 seconds total)