Starting phenix.real_space_refine on Wed Jan 17 12:00:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2q_31660/01_2024/7v2q_31660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2q_31660/01_2024/7v2q_31660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2q_31660/01_2024/7v2q_31660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2q_31660/01_2024/7v2q_31660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2q_31660/01_2024/7v2q_31660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2q_31660/01_2024/7v2q_31660.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1391 5.49 5 S 61 5.16 5 C 27825 2.51 5 N 9910 2.21 5 O 13715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 38": "OE1" <-> "OE2" Residue "U GLU 143": "OE1" <-> "OE2" Residue "U GLU 160": "OE1" <-> "OE2" Residue "W GLU 48": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 143": "OE1" <-> "OE2" Residue "W GLU 170": "OE1" <-> "OE2" Residue "W GLU 183": "OE1" <-> "OE2" Residue "W GLU 279": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 52904 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 29898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1391, 29898 Classifications: {'RNA': 1391} Modifications used: {'rna2p_pur': 115, 'rna2p_pyr': 88, 'rna3p_pur': 673, 'rna3p_pyr': 515} Link IDs: {'rna2p': 203, 'rna3p': 1187} Chain breaks: 2 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: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2013 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 12, 'TRANS': 244} 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: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2023 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} 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 33371 SG CYS D 9 91.723 71.062 96.951 1.00 54.19 S ATOM 33396 SG CYS D 12 93.023 73.966 98.502 1.00 54.90 S ATOM 33514 SG CYS D 26 94.931 70.397 97.563 1.00 59.14 S ATOM 33554 SG CYS D 31 95.915 73.122 95.478 1.00 62.94 S ATOM 44132 SG CYS N 24 63.656 122.843 49.690 1.00 64.08 S ATOM 44156 SG CYS N 27 61.756 121.532 52.728 1.00 62.65 S ATOM 44263 SG CYS N 40 63.100 124.955 53.009 1.00 58.16 S ATOM 44288 SG CYS N 43 65.496 122.586 53.251 1.00 58.79 S Time building chain proxies: 20.99, per 1000 atoms: 0.40 Number of scatterers: 52904 At special positions: 0 Unit cell: (142.14, 211.14, 230.46, 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 1391 15.00 O 13715 8.00 N 9910 7.00 C 27825 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: 19.86 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 12 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 31 " 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 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 12 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5336 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 26 sheets defined 43.2% alpha, 17.3% beta 461 base pairs and 708 stacking pairs defined. Time for finding SS restraints: 17.57 Creating SS restraints... Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.619A pdb=" N GLY B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.482A 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 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 104 through 123 removed outlier: 3.676A pdb=" N ALA B 123 " --> pdb=" O GLU B 119 " (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 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.615A pdb=" N ILE B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.851A pdb=" N LEU C 12 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 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: 4.288A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) 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: 3.850A pdb=" N SER C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.726A pdb=" N GLY C 159 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.650A pdb=" N CYS D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.659A pdb=" N TYR D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 removed outlier: 3.541A pdb=" N LYS D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 113 through 123 removed outlier: 3.670A pdb=" N GLN D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 153 Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.886A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 103 through 113 removed outlier: 3.714A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 113 " --> pdb=" O ILE E 109 " (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: 3.750A 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: 3.908A pdb=" N THR G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.533A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 removed outlier: 3.837A pdb=" N VAL G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 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: 4.374A 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 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: 3.992A 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 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'J' and resid 12 through 30 Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'K' and resid 44 through 49 Processing helix chain 'K' and resid 51 through 56 removed outlier: 3.998A pdb=" N ARG K 54 " --> pdb=" O LYS K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 74 removed outlier: 3.715A pdb=" N ALA K 61 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 100 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'L' and resid 3 through 11 Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.822A pdb=" N GLY M 38 " --> pdb=" O LEU M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 64 removed outlier: 4.176A pdb=" N TRP M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.629A 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 removed outlier: 3.532A pdb=" N ALA N 10 " --> pdb=" O LEU N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 removed outlier: 3.590A 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: 3.914A pdb=" N HIS O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 3.889A 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: 4.165A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.515A pdb=" N SER Q 99 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 42 through 44 No H-bonds generated for 'chain 'R' and resid 42 through 44' Processing helix chain 'R' and resid 52 through 57 Processing helix chain 'R' and resid 59 through 76 Processing helix chain 'S' and resid 12 through 25 removed outlier: 3.873A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 75 removed outlier: 3.649A pdb=" N PHE S 74 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.776A pdb=" N ARG T 17 " --> pdb=" O LEU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 69 removed outlier: 3.849A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 92 Processing helix chain 'U' and resid 35 through 43 removed outlier: 4.439A pdb=" N ARG U 39 " --> pdb=" O ASN U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 68 removed outlier: 4.142A pdb=" N LYS U 68 " --> pdb=" O GLU U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 90 removed outlier: 3.647A pdb=" N ASP U 88 " --> pdb=" O PRO U 84 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR U 89 " --> pdb=" O ILE U 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 116 Processing helix chain 'U' and resid 129 through 143 removed outlier: 3.957A pdb=" N THR U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) Proline residue: U 135 - end of helix removed outlier: 3.876A pdb=" N MET U 138 " --> pdb=" O THR U 134 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU U 143 " --> pdb=" O LYS U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.671A pdb=" N TYR U 181 " --> pdb=" O ALA U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 233 Processing helix chain 'U' and resid 238 through 246 Processing helix chain 'U' and resid 250 through 252 No H-bonds generated for 'chain 'U' and resid 250 through 252' Processing helix chain 'U' and resid 253 through 264 Processing helix chain 'U' and resid 276 through 288 Processing helix chain 'V' and resid 8 through 16 Processing helix chain 'W' and resid 35 through 44 Processing helix chain 'W' and resid 60 through 68 removed outlier: 3.644A pdb=" N LYS W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 90 removed outlier: 3.534A pdb=" N LEU W 90 " --> pdb=" O LEU W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 116 Processing helix chain 'W' and resid 133 through 143 removed outlier: 3.619A pdb=" N ILE W 137 " --> pdb=" O THR W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 163 Processing helix chain 'W' and resid 172 through 180 removed outlier: 3.526A pdb=" N ILE W 176 " --> pdb=" O GLY W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 220 through 232 Processing helix chain 'W' and resid 238 through 247 removed outlier: 3.686A pdb=" N LEU W 247 " --> pdb=" O LEU W 243 " (cutoff:3.500A) Processing helix chain 'W' and resid 253 through 264 removed outlier: 4.006A pdb=" N ILE W 257 " --> pdb=" O GLN W 253 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 286 removed outlier: 3.503A pdb=" N LEU W 283 " --> pdb=" O GLU W 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 removed outlier: 7.294A pdb=" N ILE B 41 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 8.029A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 69 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 6.143A 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: 3.818A pdb=" N ARG C 59 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN C 102 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLN C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL C 68 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 6.619A pdb=" N LEU E 31 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE E 13 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY E 29 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG E 15 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG E 27 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA E 17 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG E 25 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET E 19 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY E 23 " --> pdb=" O MET E 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 removed outlier: 7.013A pdb=" N ILE E 101 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLU E 122 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 45 removed outlier: 6.994A pdb=" N GLN F 64 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL F 40 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TRP F 62 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLU F 42 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE F 60 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ARG F 3 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LYS F 92 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU F 5 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN F 7 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL F 88 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.994A pdb=" N ALA F 99 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE R 29 " --> pdb=" O ALA F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 73 through 76 Processing sheet with id=AB2, first strand: chain 'G' and resid 79 through 80 removed outlier: 3.588A pdb=" N VAL G 80 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB4, first strand: chain 'H' and resid 83 through 85 Processing sheet with id=AB5, first strand: chain 'H' and resid 83 through 85 removed outlier: 5.693A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS H 135 " --> pdb=" O ILE H 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 4 through 6 removed outlier: 6.560A pdb=" N THR I 27 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 9 through 10 Processing sheet with id=AB8, first strand: chain 'J' and resid 40 through 49 removed outlier: 5.665A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU J 8 " --> pdb=" O ARG J 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 40 through 49 removed outlier: 5.665A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 39 through 41 removed outlier: 3.753A pdb=" N THR K 41 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 80 " --> pdb=" O VAL K 105 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER K 107 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.527A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL L 36 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 49 through 51 removed outlier: 5.778A pdb=" N LYS P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL P 2 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 5 through 15 removed outlier: 14.582A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.894A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Q 9 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP Q 13 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR Q 18 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LYS Q 69 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU Q 43 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL Q 73 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE Q 60 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL Q 56 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP Q 55 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 31 through 33 removed outlier: 3.757A pdb=" N ILE S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 96 through 99 removed outlier: 6.743A pdb=" N VAL U 73 " --> pdb=" O THR U 97 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE U 99 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA U 75 " --> pdb=" O ILE U 99 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY U 51 " --> pdb=" O MET U 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 151 through 155 removed outlier: 3.887A pdb=" N MET U 188 " --> pdb=" O VAL U 205 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG U 207 " --> pdb=" O THR U 186 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR U 186 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE U 209 " --> pdb=" O ALA U 184 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA U 184 " --> pdb=" O ILE U 209 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 96 through 99 removed outlier: 6.392A pdb=" N VAL W 73 " --> pdb=" O THR W 97 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE W 99 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA W 75 " --> pdb=" O ILE W 99 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLY W 51 " --> pdb=" O MET W 123 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL W 125 " --> pdb=" O GLY W 51 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE W 53 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE W 122 " --> pdb=" O GLY W 149 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL W 151 " --> pdb=" O ILE W 122 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL W 124 " --> pdb=" O VAL W 151 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET W 188 " --> pdb=" O VAL W 205 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG W 207 " --> pdb=" O THR W 186 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR W 186 " --> pdb=" O ARG W 207 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE W 209 " --> pdb=" O ALA W 184 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA W 184 " --> pdb=" O ILE W 209 " (cutoff:3.500A) 1019 hydrogen bonds defined for protein. 2892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1220 hydrogen bonds 2004 hydrogen bond angles 0 basepair planarities 461 basepair parallelities 708 stacking parallelities Total time for adding SS restraints: 36.08 Time building geometry restraints manager: 21.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7660 1.33 - 1.46: 24865 1.46 - 1.58: 21417 1.58 - 1.70: 2779 1.70 - 1.82: 107 Bond restraints: 56828 Sorted by residual: bond pdb=" N GLY C 2 " pdb=" CA GLY C 2 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.42e+00 bond pdb=" CA SER W 276 " pdb=" CB SER W 276 " ideal model delta sigma weight residual 1.528 1.491 0.037 1.48e-02 4.57e+03 6.29e+00 bond pdb=" C TYR D 38 " pdb=" N PRO D 39 " ideal model delta sigma weight residual 1.329 1.359 -0.030 1.18e-02 7.18e+03 6.28e+00 bond pdb=" O5' G A 243 " pdb=" C5' G A 243 " ideal model delta sigma weight residual 1.420 1.457 -0.037 1.50e-02 4.44e+03 6.01e+00 bond pdb=" N GLY V 2 " pdb=" CA GLY V 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.96e+00 ... (remaining 56823 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.48: 8759 106.48 - 113.49: 31557 113.49 - 120.50: 24589 120.50 - 127.51: 16103 127.51 - 134.52: 2614 Bond angle restraints: 83622 Sorted by residual: angle pdb=" O3' U A 825 " pdb=" C3' U A 825 " pdb=" C2' U A 825 " ideal model delta sigma weight residual 109.50 118.69 -9.19 1.50e+00 4.44e-01 3.75e+01 angle pdb=" O3' A A1084 " pdb=" C3' A A1084 " pdb=" C2' A A1084 " ideal model delta sigma weight residual 109.50 118.41 -8.91 1.50e+00 4.44e-01 3.53e+01 angle pdb=" C4' G A1036 " pdb=" C3' G A1036 " pdb=" O3' G A1036 " ideal model delta sigma weight residual 109.40 117.91 -8.51 1.50e+00 4.44e-01 3.22e+01 angle pdb=" C4' U A 862 " pdb=" C3' U A 862 " pdb=" O3' U A 862 " ideal model delta sigma weight residual 109.40 117.77 -8.37 1.50e+00 4.44e-01 3.11e+01 angle pdb=" C4' G A 124 " pdb=" C3' G A 124 " pdb=" O3' G A 124 " ideal model delta sigma weight residual 109.40 117.41 -8.01 1.50e+00 4.44e-01 2.85e+01 ... (remaining 83617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 32189 35.94 - 71.89: 3124 71.89 - 107.83: 462 107.83 - 143.78: 12 143.78 - 179.72: 13 Dihedral angle restraints: 35800 sinusoidal: 27518 harmonic: 8282 Sorted by residual: dihedral pdb=" C5' A A 717 " pdb=" C4' A A 717 " pdb=" C3' A A 717 " pdb=" O3' A A 717 " ideal model delta sinusoidal sigma weight residual 147.00 79.16 67.84 1 8.00e+00 1.56e-02 9.34e+01 dihedral pdb=" O4' C A 326 " pdb=" C1' C A 326 " pdb=" N1 C A 326 " pdb=" C2 C A 326 " ideal model delta sinusoidal sigma weight residual 200.00 28.08 171.92 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" C4' A A 717 " pdb=" C3' A A 717 " pdb=" C2' A A 717 " pdb=" C1' A A 717 " ideal model delta sinusoidal sigma weight residual -35.00 28.91 -63.91 1 8.00e+00 1.56e-02 8.40e+01 ... (remaining 35797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 6952 0.107 - 0.215: 2909 0.215 - 0.322: 570 0.322 - 0.429: 10 0.429 - 0.537: 3 Chirality restraints: 10444 Sorted by residual: chirality pdb=" C3' A A1084 " pdb=" C4' A A1084 " pdb=" O3' A A1084 " pdb=" C2' A A1084 " both_signs ideal model delta sigma weight residual False -2.74 -2.21 -0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" C3' A A 717 " pdb=" C4' A A 717 " pdb=" O3' A A 717 " pdb=" C2' A A 717 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" C3' U A 825 " pdb=" C4' U A 825 " pdb=" O3' U A 825 " pdb=" C2' U A 825 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 10441 not shown) Planarity restraints: 5449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 71 " -0.006 2.00e-02 2.50e+03 2.03e-02 1.24e+01 pdb=" N9 G A 71 " -0.004 2.00e-02 2.50e+03 pdb=" C8 G A 71 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G A 71 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 71 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G A 71 " 0.028 2.00e-02 2.50e+03 pdb=" O6 G A 71 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G A 71 " -0.048 2.00e-02 2.50e+03 pdb=" C2 G A 71 " 0.039 2.00e-02 2.50e+03 pdb=" N2 G A 71 " -0.010 2.00e-02 2.50e+03 pdb=" N3 G A 71 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 71 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 864 " -0.005 2.00e-02 2.50e+03 1.95e-02 1.14e+01 pdb=" N9 G A 864 " -0.005 2.00e-02 2.50e+03 pdb=" C8 G A 864 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G A 864 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 864 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 864 " -0.013 2.00e-02 2.50e+03 pdb=" O6 G A 864 " 0.020 2.00e-02 2.50e+03 pdb=" N1 G A 864 " -0.044 2.00e-02 2.50e+03 pdb=" C2 G A 864 " 0.043 2.00e-02 2.50e+03 pdb=" N2 G A 864 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G A 864 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 864 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 872 " -0.001 2.00e-02 2.50e+03 1.72e-02 8.90e+00 pdb=" N9 G A 872 " -0.001 2.00e-02 2.50e+03 pdb=" C8 G A 872 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G A 872 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 872 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G A 872 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G A 872 " -0.023 2.00e-02 2.50e+03 pdb=" N1 G A 872 " 0.041 2.00e-02 2.50e+03 pdb=" C2 G A 872 " -0.033 2.00e-02 2.50e+03 pdb=" N2 G A 872 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 872 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G A 872 " -0.003 2.00e-02 2.50e+03 ... (remaining 5446 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4604 2.73 - 3.27: 48221 3.27 - 3.82: 102542 3.82 - 4.36: 127043 4.36 - 4.90: 177474 Nonbonded interactions: 459884 Sorted by model distance: nonbonded pdb=" OP2 U A 959 " pdb=" O2' U A 960 " model vdw 2.189 2.440 nonbonded pdb=" OD1 ASP G 15 " pdb=" N LEU G 16 " model vdw 2.216 2.520 nonbonded pdb=" OG1 THR U 193 " pdb=" O VAL U 196 " model vdw 2.233 2.440 nonbonded pdb=" O2 U A 661 " pdb=" O2' A A 761 " model vdw 2.233 2.440 nonbonded pdb=" N2 G A1248 " pdb=" OP2 A A1251 " model vdw 2.252 2.520 ... (remaining 459879 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 34 through 288) selection = (chain 'W' and resid 34 through 288) } 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: 1.540 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: 0.050 Extract box with map and model: 8.770 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 143.680 Find NCS groups from input model: 1.150 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 56828 Z= 0.486 Angle : 1.135 9.191 83622 Z= 0.715 Chirality : 0.105 0.537 10444 Planarity : 0.004 0.027 5449 Dihedral : 22.478 179.719 30464 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.36 % Favored : 93.57 % Rotamer: Outliers : 0.16 % Allowed : 4.62 % Favored : 95.22 % Cbeta Deviations : 0.07 % 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: -1.01 (0.15), residues: 2831 helix: 0.25 (0.15), residues: 1134 sheet: -0.16 (0.24), residues: 468 loop : -1.74 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 42 HIS 0.008 0.002 HIS P 13 PHE 0.018 0.003 PHE U 180 TYR 0.030 0.002 TYR U 171 ARG 0.012 0.001 ARG U 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 538 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8664 (ttm) cc_final: 0.8366 (ttm) REVERT: B 128 GLU cc_start: 0.7863 (mp0) cc_final: 0.7548 (mp0) REVERT: C 93 LYS cc_start: 0.8407 (tptp) cc_final: 0.8097 (ptpt) REVERT: D 47 ARG cc_start: 0.6592 (mpt180) cc_final: 0.6391 (tpp-160) REVERT: D 151 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8243 (mtmt) REVERT: D 166 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7590 (ttpp) REVERT: D 177 ASP cc_start: 0.7493 (t0) cc_final: 0.6175 (t70) REVERT: E 145 LYS cc_start: 0.8432 (tppp) cc_final: 0.8190 (tptp) REVERT: F 16 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8033 (mm-40) REVERT: F 47 ARG cc_start: 0.8374 (tpp80) cc_final: 0.8133 (mmm-85) REVERT: F 55 ASP cc_start: 0.6928 (t0) cc_final: 0.6562 (t0) REVERT: G 15 ASP cc_start: 0.6811 (t0) cc_final: 0.5824 (p0) REVERT: G 20 ASP cc_start: 0.7467 (t70) cc_final: 0.7232 (t70) REVERT: G 68 ASN cc_start: 0.8832 (t0) cc_final: 0.8596 (t0) REVERT: G 73 MET cc_start: 0.7345 (mmp) cc_final: 0.6634 (mtm) REVERT: G 85 TYR cc_start: 0.6777 (m-80) cc_final: 0.6338 (m-80) REVERT: G 126 ASP cc_start: 0.7952 (m-30) cc_final: 0.7594 (m-30) REVERT: G 129 GLU cc_start: 0.7820 (tp30) cc_final: 0.7182 (tm-30) REVERT: H 42 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8102 (mm-30) REVERT: I 32 ASP cc_start: 0.8805 (t70) cc_final: 0.8556 (t0) REVERT: I 51 ARG cc_start: 0.7505 (ptp90) cc_final: 0.7265 (ptp-110) REVERT: I 64 THR cc_start: 0.8050 (m) cc_final: 0.7783 (p) REVERT: J 23 ILE cc_start: 0.8303 (mm) cc_final: 0.7854 (tt) REVERT: J 38 ILE cc_start: 0.7832 (mm) cc_final: 0.7614 (mm) REVERT: J 82 ILE cc_start: 0.8527 (mm) cc_final: 0.8326 (mm) REVERT: J 86 MET cc_start: 0.8037 (mpp) cc_final: 0.7704 (mpp) REVERT: K 50 TYR cc_start: 0.6150 (m-80) cc_final: 0.5871 (m-80) REVERT: K 57 THR cc_start: 0.7129 (m) cc_final: 0.6735 (p) REVERT: K 92 GLU cc_start: 0.7294 (pm20) cc_final: 0.7093 (mm-30) REVERT: K 114 VAL cc_start: 0.8711 (m) cc_final: 0.8392 (t) REVERT: M 79 LYS cc_start: 0.8105 (ptmm) cc_final: 0.7774 (mmmt) REVERT: M 82 MET cc_start: 0.7595 (tpt) cc_final: 0.7377 (tpp) REVERT: N 8 GLU cc_start: 0.8115 (mp0) cc_final: 0.7775 (mp0) REVERT: O 4 THR cc_start: 0.8551 (p) cc_final: 0.8050 (p) REVERT: O 6 GLU cc_start: 0.8390 (mp0) cc_final: 0.8087 (pm20) REVERT: O 13 GLN cc_start: 0.8463 (pm20) cc_final: 0.7942 (pm20) REVERT: O 14 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7700 (tm-30) REVERT: P 52 ASP cc_start: 0.8708 (t0) cc_final: 0.7988 (t70) REVERT: Q 36 ILE cc_start: 0.9159 (mm) cc_final: 0.8886 (mm) REVERT: Q 82 MET cc_start: 0.8711 (tpp) cc_final: 0.8482 (tpp) REVERT: Q 90 ILE cc_start: 0.8662 (mt) cc_final: 0.8452 (mt) REVERT: Q 93 GLN cc_start: 0.8495 (tt0) cc_final: 0.8151 (tp40) REVERT: R 41 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8278 (mtmm) REVERT: R 46 GLU cc_start: 0.7446 (pm20) cc_final: 0.6797 (mp0) REVERT: R 86 VAL cc_start: 0.7019 (m) cc_final: 0.6549 (p) REVERT: U 131 TYR cc_start: 0.6758 (p90) cc_final: 0.6301 (p90) REVERT: W 39 ARG cc_start: 0.8342 (ttm110) cc_final: 0.8118 (ttm110) REVERT: W 100 HIS cc_start: 0.7402 (t-90) cc_final: 0.7101 (t-90) outliers start: 4 outliers final: 0 residues processed: 540 average time/residue: 0.5816 time to fit residues: 496.8322 Evaluate side-chains 353 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 326 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 242 optimal weight: 0.7980 chunk 377 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 102 ASN C 108 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN G 97 GLN I 58 HIS J 76 ASN J 84 GLN K 38 ASN S 69 HIS T 90 GLN U 35 ASN U 200 ASN W 198 GLN W 234 GLN W 242 ASN W 265 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 56828 Z= 0.208 Angle : 0.575 10.072 83622 Z= 0.296 Chirality : 0.036 0.307 10444 Planarity : 0.005 0.045 5449 Dihedral : 23.242 179.194 24519 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.77 % Rotamer: Outliers : 1.65 % Allowed : 10.60 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2831 helix: 1.11 (0.16), residues: 1140 sheet: -0.05 (0.25), residues: 475 loop : -1.32 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 103 HIS 0.004 0.001 HIS L 96 PHE 0.024 0.002 PHE R 81 TYR 0.020 0.002 TYR P 32 ARG 0.012 0.001 ARG M 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 355 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8709 (ttm) cc_final: 0.8282 (ttm) REVERT: B 128 GLU cc_start: 0.7933 (mp0) cc_final: 0.7716 (mp0) REVERT: C 93 LYS cc_start: 0.8542 (tptp) cc_final: 0.8134 (ptpt) REVERT: D 49 ARG cc_start: 0.7052 (tpt170) cc_final: 0.6805 (tpm170) REVERT: D 166 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7574 (ttpp) REVERT: D 177 ASP cc_start: 0.7389 (t0) cc_final: 0.6840 (t70) REVERT: E 145 LYS cc_start: 0.8303 (tppp) cc_final: 0.8068 (tptp) REVERT: F 16 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8307 (mm-40) REVERT: F 25 ILE cc_start: 0.8729 (tp) cc_final: 0.8385 (pt) REVERT: F 27 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8329 (mm-40) REVERT: F 47 ARG cc_start: 0.8355 (tpp80) cc_final: 0.8076 (mmm-85) REVERT: G 20 ASP cc_start: 0.7737 (t70) cc_final: 0.7338 (t70) REVERT: G 22 LEU cc_start: 0.8384 (mm) cc_final: 0.7878 (mp) REVERT: G 31 MET cc_start: 0.7852 (ttm) cc_final: 0.7527 (ttp) REVERT: G 68 ASN cc_start: 0.8743 (t0) cc_final: 0.8538 (t0) REVERT: G 85 TYR cc_start: 0.6718 (m-80) cc_final: 0.6507 (m-80) REVERT: G 129 GLU cc_start: 0.7893 (tp30) cc_final: 0.7114 (tm-30) REVERT: H 9 MET cc_start: 0.8769 (ttp) cc_final: 0.8514 (ttm) REVERT: I 32 ASP cc_start: 0.8699 (t70) cc_final: 0.8308 (t0) REVERT: I 35 GLU cc_start: 0.8348 (pt0) cc_final: 0.7888 (tp30) REVERT: I 47 LEU cc_start: 0.7902 (mt) cc_final: 0.7526 (pp) REVERT: I 51 ARG cc_start: 0.7460 (ptp90) cc_final: 0.7028 (ptp90) REVERT: I 127 LYS cc_start: 0.6782 (tptt) cc_final: 0.6296 (tmmt) REVERT: J 23 ILE cc_start: 0.8424 (mm) cc_final: 0.7965 (tt) REVERT: J 86 MET cc_start: 0.7957 (mpp) cc_final: 0.7646 (mpp) REVERT: K 57 THR cc_start: 0.6595 (m) cc_final: 0.6310 (p) REVERT: K 63 LEU cc_start: 0.7522 (mt) cc_final: 0.7073 (mp) REVERT: K 66 LEU cc_start: 0.7439 (mt) cc_final: 0.7096 (pp) REVERT: K 92 GLU cc_start: 0.7373 (pm20) cc_final: 0.7083 (mm-30) REVERT: M 32 GLU cc_start: 0.8463 (pp20) cc_final: 0.8256 (pp20) REVERT: M 34 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5776 (tt) REVERT: M 57 ARG cc_start: 0.7804 (ptp-110) cc_final: 0.7423 (ptp-110) REVERT: M 79 LYS cc_start: 0.8084 (ptmm) cc_final: 0.7805 (mmmt) REVERT: M 105 THR cc_start: 0.8425 (p) cc_final: 0.8211 (p) REVERT: O 14 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7786 (tm-30) REVERT: Q 93 GLN cc_start: 0.8546 (tt0) cc_final: 0.8134 (tp40) REVERT: Q 96 GLU cc_start: 0.7993 (mp0) cc_final: 0.7627 (mp0) REVERT: R 41 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7945 (mtmm) REVERT: R 46 GLU cc_start: 0.7473 (pm20) cc_final: 0.6979 (mp0) REVERT: R 62 GLU cc_start: 0.7777 (pt0) cc_final: 0.7565 (mt-10) REVERT: R 86 VAL cc_start: 0.7140 (m) cc_final: 0.6723 (p) REVERT: S 6 LYS cc_start: 0.7358 (mttp) cc_final: 0.7072 (ptpp) REVERT: W 39 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8081 (ttm110) REVERT: W 100 HIS cc_start: 0.7276 (t-90) cc_final: 0.6813 (t-90) REVERT: W 162 MET cc_start: 0.7150 (mtt) cc_final: 0.6928 (mtt) outliers start: 40 outliers final: 22 residues processed: 383 average time/residue: 0.5534 time to fit residues: 344.4518 Evaluate side-chains 337 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 314 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain U residue 132 VAL Chi-restraints excluded: chain U residue 222 SER Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 202 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 314 optimal weight: 0.0370 chunk 257 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 408 optimal weight: 3.9990 chunk 337 optimal weight: 4.9990 chunk 375 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN F 18 GLN G 122 HIS J 76 ASN J 84 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN W 198 GLN ** W 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 56828 Z= 0.332 Angle : 0.656 9.521 83622 Z= 0.334 Chirality : 0.040 0.273 10444 Planarity : 0.005 0.062 5449 Dihedral : 23.318 179.832 24519 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 2.52 % Allowed : 13.36 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2831 helix: 0.90 (0.15), residues: 1168 sheet: -0.20 (0.24), residues: 472 loop : -1.31 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 24 HIS 0.008 0.002 HIS S 57 PHE 0.028 0.002 PHE J 54 TYR 0.025 0.002 TYR P 32 ARG 0.011 0.001 ARG L 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 318 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.8002 (mp0) cc_final: 0.7699 (mp0) REVERT: C 93 LYS cc_start: 0.8701 (tptp) cc_final: 0.8225 (ptpt) REVERT: D 166 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7772 (ttpp) REVERT: D 177 ASP cc_start: 0.7418 (t0) cc_final: 0.7151 (t70) REVERT: E 12 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8736 (pt) REVERT: E 145 LYS cc_start: 0.8461 (tppp) cc_final: 0.8228 (tptp) REVERT: F 25 ILE cc_start: 0.8714 (tp) cc_final: 0.8448 (pt) REVERT: F 47 ARG cc_start: 0.8378 (tpp80) cc_final: 0.8168 (mmm-85) REVERT: G 22 LEU cc_start: 0.8333 (mm) cc_final: 0.7879 (mp) REVERT: G 85 TYR cc_start: 0.6618 (m-80) cc_final: 0.6406 (m-80) REVERT: G 129 GLU cc_start: 0.8024 (tp30) cc_final: 0.7254 (tm-30) REVERT: I 20 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6364 (mpt180) REVERT: I 35 GLU cc_start: 0.8175 (pt0) cc_final: 0.7830 (tp30) REVERT: I 110 GLU cc_start: 0.8619 (tt0) cc_final: 0.8278 (tt0) REVERT: I 127 LYS cc_start: 0.6717 (tptt) cc_final: 0.6516 (tmmt) REVERT: J 86 MET cc_start: 0.7565 (mpp) cc_final: 0.7303 (mpp) REVERT: K 38 ASN cc_start: 0.7969 (m-40) cc_final: 0.7752 (m110) REVERT: K 57 THR cc_start: 0.6894 (m) cc_final: 0.6569 (p) REVERT: K 63 LEU cc_start: 0.7728 (mt) cc_final: 0.7521 (mt) REVERT: K 66 LEU cc_start: 0.7583 (mt) cc_final: 0.7281 (pp) REVERT: K 77 MET cc_start: 0.5975 (ppp) cc_final: 0.5453 (tmm) REVERT: M 32 GLU cc_start: 0.8158 (pp20) cc_final: 0.7873 (pp20) REVERT: M 34 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5883 (tt) REVERT: M 105 THR cc_start: 0.8422 (p) cc_final: 0.8222 (p) REVERT: O 14 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7578 (tm-30) REVERT: P 47 ASP cc_start: 0.8424 (p0) cc_final: 0.8193 (p0) REVERT: Q 36 ILE cc_start: 0.9327 (mm) cc_final: 0.9096 (mm) REVERT: Q 93 GLN cc_start: 0.8483 (tt0) cc_final: 0.8243 (tt0) REVERT: R 36 ASN cc_start: 0.8165 (t0) cc_final: 0.7853 (t0) REVERT: R 46 GLU cc_start: 0.7786 (pm20) cc_final: 0.7333 (mp0) REVERT: U 69 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7709 (mmm160) REVERT: U 209 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7700 (pt) REVERT: U 288 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: W 100 HIS cc_start: 0.7274 (t-90) cc_final: 0.6809 (t-90) REVERT: W 162 MET cc_start: 0.7164 (mtt) cc_final: 0.6917 (mtt) REVERT: W 181 TYR cc_start: 0.7297 (m-80) cc_final: 0.6841 (m-10) outliers start: 61 outliers final: 29 residues processed: 358 average time/residue: 0.5419 time to fit residues: 317.2066 Evaluate side-chains 318 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 284 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain U residue 138 MET Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 209 ILE Chi-restraints excluded: chain U residue 288 TYR Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 202 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 chunk 196 optimal weight: 0.4980 chunk 41 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 chunk 402 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN G 122 HIS J 76 ASN J 84 GLN ** W 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 56828 Z= 0.324 Angle : 0.638 10.661 83622 Z= 0.324 Chirality : 0.039 0.263 10444 Planarity : 0.005 0.052 5449 Dihedral : 23.302 178.872 24519 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 2.93 % Allowed : 15.22 % Favored : 81.86 % 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: -0.30 (0.16), residues: 2831 helix: 0.93 (0.15), residues: 1167 sheet: -0.29 (0.24), residues: 476 loop : -1.28 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 138 HIS 0.006 0.001 HIS S 57 PHE 0.021 0.002 PHE H 31 TYR 0.023 0.002 TYR P 32 ARG 0.011 0.001 ARG W 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 313 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8181 (ttm) cc_final: 0.7928 (mtm) REVERT: B 128 GLU cc_start: 0.7928 (mp0) cc_final: 0.7678 (mp0) REVERT: C 93 LYS cc_start: 0.8883 (tptp) cc_final: 0.8348 (ptpt) REVERT: C 178 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8572 (mm) REVERT: D 166 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7657 (ttpp) REVERT: D 177 ASP cc_start: 0.7366 (t0) cc_final: 0.7071 (t70) REVERT: E 12 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8681 (pt) REVERT: E 145 LYS cc_start: 0.8428 (tppp) cc_final: 0.8218 (tptp) REVERT: F 25 ILE cc_start: 0.8680 (tp) cc_final: 0.8381 (pt) REVERT: F 83 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7605 (p0) REVERT: G 22 LEU cc_start: 0.8259 (mm) cc_final: 0.7830 (mp) REVERT: G 85 TYR cc_start: 0.6714 (m-80) cc_final: 0.6266 (m-80) REVERT: G 129 GLU cc_start: 0.8042 (tp30) cc_final: 0.7251 (tm-30) REVERT: I 20 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6250 (mpt180) REVERT: I 35 GLU cc_start: 0.8133 (pt0) cc_final: 0.7849 (tp30) REVERT: I 110 GLU cc_start: 0.8615 (tt0) cc_final: 0.8318 (tt0) REVERT: K 57 THR cc_start: 0.6864 (m) cc_final: 0.6644 (p) REVERT: K 66 LEU cc_start: 0.7637 (mt) cc_final: 0.7262 (pp) REVERT: K 77 MET cc_start: 0.5857 (ppp) cc_final: 0.5387 (tmm) REVERT: M 32 GLU cc_start: 0.8045 (pp20) cc_final: 0.7664 (pp20) REVERT: M 34 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5460 (tt) REVERT: O 41 GLU cc_start: 0.8307 (mp0) cc_final: 0.7962 (mp0) REVERT: R 36 ASN cc_start: 0.8137 (t0) cc_final: 0.7774 (t0) REVERT: R 46 GLU cc_start: 0.7802 (pm20) cc_final: 0.7353 (mp0) REVERT: U 69 ARG cc_start: 0.7873 (mmm160) cc_final: 0.7607 (mmm160) REVERT: U 76 PHE cc_start: 0.7017 (m-80) cc_final: 0.6582 (m-80) REVERT: U 179 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: U 209 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7775 (pt) REVERT: U 288 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: W 100 HIS cc_start: 0.7430 (t-90) cc_final: 0.7195 (t-90) REVERT: W 101 GLN cc_start: 0.7610 (tp40) cc_final: 0.7194 (tp-100) REVERT: W 162 MET cc_start: 0.7269 (mtt) cc_final: 0.6975 (mtt) REVERT: W 181 TYR cc_start: 0.7337 (m-80) cc_final: 0.6870 (m-10) REVERT: W 253 GLN cc_start: 0.4930 (mt0) cc_final: 0.3937 (pm20) outliers start: 71 outliers final: 46 residues processed: 364 average time/residue: 0.5533 time to fit residues: 330.9078 Evaluate side-chains 343 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 289 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 43 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 179 GLN Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain U residue 195 PHE Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 209 ILE Chi-restraints excluded: chain U residue 288 TYR Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 153 MET Chi-restraints excluded: chain W residue 202 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 343 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 360 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS J 76 ASN J 84 GLN K 38 ASN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 56828 Z= 0.243 Angle : 0.589 10.146 83622 Z= 0.301 Chirality : 0.037 0.252 10444 Planarity : 0.005 0.047 5449 Dihedral : 23.269 178.672 24519 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 3.46 % Allowed : 15.92 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2831 helix: 1.10 (0.15), residues: 1164 sheet: -0.30 (0.24), residues: 476 loop : -1.23 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 138 HIS 0.006 0.001 HIS S 57 PHE 0.015 0.002 PHE H 31 TYR 0.018 0.002 TYR P 32 ARG 0.008 0.000 ARG W 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 307 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8222 (ttm) cc_final: 0.7965 (mtm) REVERT: B 76 GLN cc_start: 0.8620 (pm20) cc_final: 0.8366 (pm20) REVERT: B 128 GLU cc_start: 0.7851 (mp0) cc_final: 0.7595 (mp0) REVERT: C 93 LYS cc_start: 0.8923 (tptp) cc_final: 0.8415 (ptpt) REVERT: C 178 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8571 (mm) REVERT: D 166 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7671 (ttpp) REVERT: D 177 ASP cc_start: 0.7358 (t0) cc_final: 0.7045 (t70) REVERT: E 12 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8614 (pt) REVERT: F 23 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7414 (mtmt) REVERT: F 25 ILE cc_start: 0.8718 (tp) cc_final: 0.8453 (pt) REVERT: F 27 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8117 (mp10) REVERT: G 73 MET cc_start: 0.7582 (mmt) cc_final: 0.7343 (mmp) REVERT: G 85 TYR cc_start: 0.6585 (m-80) cc_final: 0.6203 (m-80) REVERT: G 129 GLU cc_start: 0.8040 (tp30) cc_final: 0.7229 (tm-30) REVERT: I 20 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.6092 (mpt180) REVERT: I 35 GLU cc_start: 0.8086 (pt0) cc_final: 0.7746 (tp30) REVERT: I 110 GLU cc_start: 0.8610 (tt0) cc_final: 0.8320 (tt0) REVERT: K 57 THR cc_start: 0.6892 (m) cc_final: 0.6680 (p) REVERT: K 66 LEU cc_start: 0.7542 (mt) cc_final: 0.7099 (pp) REVERT: K 77 MET cc_start: 0.6117 (ppp) cc_final: 0.5893 (tmm) REVERT: M 34 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5600 (tt) REVERT: O 41 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: R 28 GLU cc_start: 0.7775 (tt0) cc_final: 0.7569 (tt0) REVERT: R 36 ASN cc_start: 0.8085 (t0) cc_final: 0.7594 (t0) REVERT: R 46 GLU cc_start: 0.7844 (pm20) cc_final: 0.7433 (mp0) REVERT: T 51 GLU cc_start: 0.7659 (pm20) cc_final: 0.7445 (pm20) REVERT: U 76 PHE cc_start: 0.6588 (m-80) cc_final: 0.6259 (m-80) REVERT: U 179 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: U 288 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: W 100 HIS cc_start: 0.7506 (t-90) cc_final: 0.7084 (t-90) REVERT: W 162 MET cc_start: 0.7383 (mtt) cc_final: 0.7105 (mtt) REVERT: W 181 TYR cc_start: 0.7338 (m-80) cc_final: 0.6858 (m-10) REVERT: W 253 GLN cc_start: 0.4933 (mt0) cc_final: 0.3934 (pm20) outliers start: 84 outliers final: 57 residues processed: 370 average time/residue: 0.5338 time to fit residues: 325.0550 Evaluate side-chains 350 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 286 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 43 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 179 GLN Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain U residue 195 PHE Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 288 TYR Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 210 LEU Chi-restraints excluded: chain W residue 241 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 20.0000 chunk 362 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 99 optimal weight: 40.0000 chunk 402 optimal weight: 9.9990 chunk 334 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 211 optimal weight: 0.4980 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 ASN C 69 HIS ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS J 84 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 56828 Z= 0.350 Angle : 0.662 10.424 83622 Z= 0.335 Chirality : 0.040 0.267 10444 Planarity : 0.005 0.052 5449 Dihedral : 23.308 179.045 24519 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.32 % Favored : 93.64 % Rotamer: Outliers : 3.84 % Allowed : 16.45 % Favored : 79.71 % 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: -0.37 (0.16), residues: 2831 helix: 0.93 (0.15), residues: 1169 sheet: -0.45 (0.24), residues: 477 loop : -1.33 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 24 HIS 0.007 0.002 HIS G 153 PHE 0.021 0.002 PHE H 31 TYR 0.023 0.002 TYR P 32 ARG 0.007 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 295 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8204 (ttm) cc_final: 0.7952 (mtm) REVERT: B 76 GLN cc_start: 0.8635 (pm20) cc_final: 0.8422 (pm20) REVERT: B 140 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7407 (m170) REVERT: C 178 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8572 (mm) REVERT: D 177 ASP cc_start: 0.7375 (t0) cc_final: 0.7075 (t70) REVERT: E 12 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8710 (pt) REVERT: F 25 ILE cc_start: 0.8756 (tp) cc_final: 0.8463 (pt) REVERT: F 83 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7466 (p0) REVERT: G 85 TYR cc_start: 0.6728 (m-80) cc_final: 0.6494 (m-80) REVERT: I 20 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5864 (mpt180) REVERT: I 110 GLU cc_start: 0.8615 (tt0) cc_final: 0.8346 (tt0) REVERT: K 66 LEU cc_start: 0.7427 (mt) cc_final: 0.7077 (pp) REVERT: K 73 MET cc_start: 0.7303 (mmm) cc_final: 0.7082 (mmm) REVERT: M 34 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5752 (tt) REVERT: M 36 LYS cc_start: 0.7682 (tmtt) cc_final: 0.7135 (ttmm) REVERT: O 41 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: R 36 ASN cc_start: 0.8074 (t0) cc_final: 0.7510 (t0) REVERT: U 69 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7772 (mmm160) REVERT: U 76 PHE cc_start: 0.6478 (m-80) cc_final: 0.6265 (m-80) REVERT: U 179 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: U 209 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7699 (pt) REVERT: U 288 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6262 (m-80) REVERT: W 100 HIS cc_start: 0.7496 (t-90) cc_final: 0.7156 (t-90) REVERT: W 162 MET cc_start: 0.7317 (mtt) cc_final: 0.7025 (mtt) REVERT: W 181 TYR cc_start: 0.7006 (m-80) cc_final: 0.6742 (m-10) REVERT: W 253 GLN cc_start: 0.5025 (mt0) cc_final: 0.3917 (pm20) outliers start: 93 outliers final: 69 residues processed: 365 average time/residue: 0.5403 time to fit residues: 324.7268 Evaluate side-chains 357 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 278 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 50 TYR Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 ASN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 43 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 154 LEU Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 179 GLN Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain U residue 195 PHE Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 209 ILE Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 288 TYR Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 210 LEU Chi-restraints excluded: chain W residue 241 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 0.0470 chunk 45 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 400 optimal weight: 5.9990 chunk 250 optimal weight: 0.1980 chunk 244 optimal weight: 2.9990 chunk 185 optimal weight: 0.0270 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN G 122 HIS J 84 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 56828 Z= 0.127 Angle : 0.534 10.255 83622 Z= 0.274 Chirality : 0.034 0.251 10444 Planarity : 0.004 0.044 5449 Dihedral : 23.190 179.621 24519 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 2.27 % Allowed : 18.23 % Favored : 79.51 % 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: 2831 helix: 1.32 (0.16), residues: 1161 sheet: -0.32 (0.24), residues: 474 loop : -1.18 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 138 HIS 0.004 0.001 HIS K 22 PHE 0.008 0.001 PHE O 15 TYR 0.014 0.001 TYR I 4 ARG 0.006 0.000 ARG U 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 315 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLU cc_start: 0.5505 (OUTLIER) cc_final: 0.5295 (pm20) REVERT: B 128 GLU cc_start: 0.7821 (mp0) cc_final: 0.7573 (mp0) REVERT: C 93 LYS cc_start: 0.8856 (tptp) cc_final: 0.8404 (ptpt) REVERT: D 177 ASP cc_start: 0.7317 (t0) cc_final: 0.6998 (t70) REVERT: F 23 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7837 (mtmt) REVERT: F 25 ILE cc_start: 0.8698 (tp) cc_final: 0.8416 (pt) REVERT: F 27 GLN cc_start: 0.8462 (tp-100) cc_final: 0.8244 (mm110) REVERT: G 13 GLN cc_start: 0.7310 (tm-30) cc_final: 0.6947 (tm-30) REVERT: G 15 ASP cc_start: 0.7701 (t0) cc_final: 0.7065 (p0) REVERT: G 85 TYR cc_start: 0.6554 (m-80) cc_final: 0.6248 (m-80) REVERT: G 129 GLU cc_start: 0.8092 (tp30) cc_final: 0.7139 (tm-30) REVERT: I 35 GLU cc_start: 0.8155 (pt0) cc_final: 0.7885 (tp30) REVERT: I 110 GLU cc_start: 0.8598 (tt0) cc_final: 0.8291 (tt0) REVERT: J 23 ILE cc_start: 0.8189 (mt) cc_final: 0.7913 (tt) REVERT: J 80 LYS cc_start: 0.7800 (tttt) cc_final: 0.7497 (tptp) REVERT: K 66 LEU cc_start: 0.7531 (mt) cc_final: 0.7197 (pp) REVERT: K 77 MET cc_start: 0.6011 (ppp) cc_final: 0.5578 (tmm) REVERT: M 34 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.6052 (tt) REVERT: M 36 LYS cc_start: 0.7738 (tmtt) cc_final: 0.7160 (ttmm) REVERT: O 41 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: R 28 GLU cc_start: 0.7683 (tt0) cc_final: 0.7447 (tt0) REVERT: R 36 ASN cc_start: 0.7956 (t0) cc_final: 0.7344 (t0) REVERT: U 288 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.6095 (m-80) REVERT: W 100 HIS cc_start: 0.7563 (t-90) cc_final: 0.7237 (t-90) REVERT: W 162 MET cc_start: 0.7418 (mtt) cc_final: 0.7164 (mtt) REVERT: W 181 TYR cc_start: 0.7229 (m-80) cc_final: 0.6549 (m-10) REVERT: W 207 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7025 (ttp-110) outliers start: 55 outliers final: 37 residues processed: 353 average time/residue: 0.5561 time to fit residues: 321.7464 Evaluate side-chains 337 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 296 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 43 LEU Chi-restraints excluded: chain U residue 154 LEU Chi-restraints excluded: chain U residue 179 GLN Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 288 TYR Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 202 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 315 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN G 122 HIS I 29 ASN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 56828 Z= 0.343 Angle : 0.651 10.598 83622 Z= 0.329 Chirality : 0.039 0.273 10444 Planarity : 0.005 0.051 5449 Dihedral : 23.243 178.294 24519 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.39 % Favored : 93.57 % Rotamer: Outliers : 3.26 % Allowed : 17.77 % Favored : 78.97 % 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: 2831 helix: 1.10 (0.16), residues: 1161 sheet: -0.40 (0.24), residues: 474 loop : -1.21 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 24 HIS 0.006 0.001 HIS S 57 PHE 0.014 0.002 PHE H 31 TYR 0.024 0.002 TYR P 32 ARG 0.007 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 289 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8204 (ttm) cc_final: 0.7885 (mtm) REVERT: B 128 GLU cc_start: 0.7896 (mp0) cc_final: 0.7601 (mp0) REVERT: B 140 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7386 (m170) REVERT: D 177 ASP cc_start: 0.7388 (t0) cc_final: 0.7056 (t70) REVERT: F 16 GLN cc_start: 0.8302 (mm110) cc_final: 0.8094 (mm110) REVERT: F 25 ILE cc_start: 0.8748 (tp) cc_final: 0.8459 (pt) REVERT: F 64 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6242 (tt0) REVERT: F 83 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7455 (p0) REVERT: I 110 GLU cc_start: 0.8610 (tt0) cc_final: 0.8338 (tt0) REVERT: K 66 LEU cc_start: 0.7427 (mt) cc_final: 0.7070 (pp) REVERT: K 98 LEU cc_start: 0.7523 (tt) cc_final: 0.7275 (tp) REVERT: M 34 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5739 (tt) REVERT: M 36 LYS cc_start: 0.7837 (tmtt) cc_final: 0.7294 (ttmm) REVERT: O 41 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: R 36 ASN cc_start: 0.7908 (t0) cc_final: 0.7242 (t0) REVERT: U 179 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: U 209 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7685 (pt) REVERT: U 288 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6215 (m-80) REVERT: W 100 HIS cc_start: 0.7681 (t-90) cc_final: 0.7416 (t-90) REVERT: W 162 MET cc_start: 0.7448 (mtt) cc_final: 0.7176 (mtt) REVERT: W 181 TYR cc_start: 0.7044 (m-80) cc_final: 0.6477 (m-10) outliers start: 79 outliers final: 56 residues processed: 348 average time/residue: 0.5472 time to fit residues: 315.3461 Evaluate side-chains 345 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 281 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 43 LEU Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 179 GLN Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain U residue 209 ILE Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 288 TYR Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 202 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 chunk 350 optimal weight: 8.9990 chunk 373 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 162 optimal weight: 0.2980 chunk 293 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 337 optimal weight: 4.9990 chunk 353 optimal weight: 8.9990 chunk 372 optimal weight: 0.9980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 122 HIS J 84 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 56828 Z= 0.204 Angle : 0.576 9.974 83622 Z= 0.294 Chirality : 0.036 0.239 10444 Planarity : 0.004 0.047 5449 Dihedral : 23.201 179.320 24519 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 2.76 % Allowed : 18.47 % Favored : 78.76 % 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: -0.12 (0.16), residues: 2831 helix: 1.19 (0.16), residues: 1162 sheet: -0.39 (0.24), residues: 476 loop : -1.20 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 138 HIS 0.004 0.001 HIS S 57 PHE 0.012 0.001 PHE H 31 TYR 0.017 0.001 TYR I 4 ARG 0.006 0.000 ARG L 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 285 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASN cc_start: 0.8024 (t0) cc_final: 0.7782 (t0) REVERT: B 63 MET cc_start: 0.8170 (ttm) cc_final: 0.7840 (mtm) REVERT: B 128 GLU cc_start: 0.7799 (mp0) cc_final: 0.7558 (mp0) REVERT: C 178 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8544 (mm) REVERT: D 177 ASP cc_start: 0.7335 (t0) cc_final: 0.7011 (t70) REVERT: E 12 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8574 (pt) REVERT: F 25 ILE cc_start: 0.8740 (tp) cc_final: 0.8444 (pt) REVERT: F 64 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6210 (tt0) REVERT: G 13 GLN cc_start: 0.7312 (tm-30) cc_final: 0.7015 (tm-30) REVERT: I 35 GLU cc_start: 0.8127 (pt0) cc_final: 0.7863 (tp30) REVERT: I 110 GLU cc_start: 0.8617 (tt0) cc_final: 0.8333 (tt0) REVERT: J 80 LYS cc_start: 0.7742 (tttt) cc_final: 0.7314 (tptp) REVERT: K 66 LEU cc_start: 0.7531 (mt) cc_final: 0.7165 (pp) REVERT: K 98 LEU cc_start: 0.7339 (tt) cc_final: 0.7082 (tp) REVERT: M 34 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5763 (tt) REVERT: M 36 LYS cc_start: 0.7896 (tmtt) cc_final: 0.7379 (ttmm) REVERT: O 41 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: R 36 ASN cc_start: 0.7800 (t0) cc_final: 0.7075 (t0) REVERT: T 42 GLN cc_start: 0.8346 (pp30) cc_final: 0.7857 (pp30) REVERT: U 179 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: U 209 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7714 (pt) REVERT: U 288 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: W 100 HIS cc_start: 0.7685 (t-90) cc_final: 0.7436 (t-90) REVERT: W 162 MET cc_start: 0.7449 (mtt) cc_final: 0.7178 (mtt) REVERT: W 181 TYR cc_start: 0.7179 (m-80) cc_final: 0.6858 (m-10) outliers start: 67 outliers final: 54 residues processed: 338 average time/residue: 0.5398 time to fit residues: 302.1050 Evaluate side-chains 343 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 281 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 43 LEU Chi-restraints excluded: chain U residue 179 GLN Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain U residue 209 ILE Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 288 TYR Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 202 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 4.9990 chunk 395 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 274 optimal weight: 20.0000 chunk 414 optimal weight: 0.9990 chunk 381 optimal weight: 0.2980 chunk 330 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 56828 Z= 0.167 Angle : 0.553 9.743 83622 Z= 0.283 Chirality : 0.035 0.261 10444 Planarity : 0.004 0.044 5449 Dihedral : 23.168 179.010 24519 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 2.60 % Allowed : 18.64 % Favored : 78.76 % 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: 2831 helix: 1.27 (0.16), residues: 1155 sheet: -0.34 (0.24), residues: 486 loop : -1.10 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 64 HIS 0.004 0.001 HIS K 22 PHE 0.018 0.001 PHE W 180 TYR 0.019 0.001 TYR I 4 ARG 0.005 0.000 ARG L 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 289 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASN cc_start: 0.8174 (t0) cc_final: 0.7968 (t0) REVERT: B 63 MET cc_start: 0.8141 (ttm) cc_final: 0.7826 (mtm) REVERT: B 128 GLU cc_start: 0.7800 (mp0) cc_final: 0.7571 (mp0) REVERT: B 140 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7373 (m170) REVERT: C 178 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8540 (mm) REVERT: D 177 ASP cc_start: 0.7333 (t0) cc_final: 0.7012 (t70) REVERT: E 12 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8503 (pt) REVERT: F 25 ILE cc_start: 0.8702 (tp) cc_final: 0.8450 (pt) REVERT: F 64 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6202 (tt0) REVERT: G 13 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6994 (tm-30) REVERT: G 22 LEU cc_start: 0.8164 (mm) cc_final: 0.7682 (tp) REVERT: I 35 GLU cc_start: 0.8130 (pt0) cc_final: 0.7873 (tp30) REVERT: I 110 GLU cc_start: 0.8621 (tt0) cc_final: 0.8311 (tt0) REVERT: J 80 LYS cc_start: 0.7743 (tttt) cc_final: 0.7314 (tptp) REVERT: K 59 TYR cc_start: 0.7934 (m-80) cc_final: 0.7705 (m-80) REVERT: K 66 LEU cc_start: 0.7484 (mt) cc_final: 0.7143 (pp) REVERT: M 34 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5767 (tt) REVERT: M 36 LYS cc_start: 0.7901 (tmtt) cc_final: 0.7373 (ttmm) REVERT: O 41 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: R 36 ASN cc_start: 0.7782 (t0) cc_final: 0.7065 (t0) REVERT: T 42 GLN cc_start: 0.8320 (pp30) cc_final: 0.8061 (pp30) REVERT: T 51 GLU cc_start: 0.7756 (pm20) cc_final: 0.7463 (pm20) REVERT: U 179 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: U 207 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7531 (ttp80) REVERT: U 209 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7716 (pt) REVERT: U 288 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: W 100 HIS cc_start: 0.7756 (t-90) cc_final: 0.7515 (t-90) REVERT: W 162 MET cc_start: 0.7468 (mtt) cc_final: 0.7200 (mtt) REVERT: W 181 TYR cc_start: 0.7196 (m-80) cc_final: 0.6535 (m-10) outliers start: 63 outliers final: 48 residues processed: 337 average time/residue: 0.5404 time to fit residues: 300.8959 Evaluate side-chains 340 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 283 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 43 LEU Chi-restraints excluded: chain U residue 179 GLN Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 209 ILE Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 288 TYR Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 202 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 304 optimal weight: 0.0870 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 339 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 84 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.046431 restraints weight = 192729.432| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.24 r_work: 0.2703 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 56828 Z= 0.276 Angle : 0.607 10.235 83622 Z= 0.308 Chirality : 0.037 0.248 10444 Planarity : 0.005 0.046 5449 Dihedral : 23.186 178.507 24519 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.53 % Favored : 93.43 % Rotamer: Outliers : 2.85 % Allowed : 18.43 % Favored : 78.72 % 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: -0.11 (0.16), residues: 2831 helix: 1.17 (0.16), residues: 1161 sheet: -0.36 (0.24), residues: 476 loop : -1.18 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 64 HIS 0.005 0.001 HIS S 57 PHE 0.014 0.002 PHE H 31 TYR 0.021 0.002 TYR P 32 ARG 0.006 0.000 ARG B 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8204.94 seconds wall clock time: 147 minutes 26.91 seconds (8846.91 seconds total)