Starting phenix.real_space_refine on Sun Feb 25 10:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2n_31657/02_2024/7v2n_31657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2n_31657/02_2024/7v2n_31657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2n_31657/02_2024/7v2n_31657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2n_31657/02_2024/7v2n_31657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2n_31657/02_2024/7v2n_31657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2n_31657/02_2024/7v2n_31657.pdb" } resolution = 3.6 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= 0.013 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 1394 5.49 5 S 55 5.16 5 C 26613 2.51 5 N 9598 2.21 5 O 13358 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 141": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 73": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51020 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 29962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1394, 29962 Classifications: {'RNA': 1394} Modifications used: {'rna2p_pur': 125, 'rna2p_pyr': 92, 'rna3p_pur': 665, 'rna3p_pyr': 512} Link IDs: {'rna2p': 216, 'rna3p': 1177} 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: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2088 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 12, 'TRANS': 253} Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33435 SG CYS D 9 94.160 74.403 94.086 1.00 76.07 S ATOM 33460 SG CYS D 12 95.231 77.300 96.419 1.00 79.67 S ATOM 33578 SG CYS D 26 97.159 73.583 95.112 1.00 84.30 S ATOM 33618 SG CYS D 31 98.207 76.381 93.778 1.00 90.88 S ATOM 44196 SG CYS N 24 62.396 123.021 50.855 1.00130.94 S ATOM 44220 SG CYS N 27 60.733 121.827 54.226 1.00129.77 S ATOM 44327 SG CYS N 40 61.895 125.536 53.706 1.00121.20 S ATOM 44352 SG CYS N 43 64.421 122.864 53.842 1.00119.17 S Time building chain proxies: 25.49, per 1000 atoms: 0.50 Number of scatterers: 51020 At special positions: 0 Unit cell: (142.14, 213.9, 226.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 55 16.00 P 1394 15.00 O 13358 8.00 N 9598 7.00 C 26613 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: 25.27 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 12 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 12 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4858 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 21 sheets defined 43.6% alpha, 18.1% beta 398 base pairs and 675 stacking pairs defined. Time for finding SS restraints: 23.76 Creating SS restraints... Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.458A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 65 Processing helix chain 'B' and resid 76 through 87 removed outlier: 4.551A pdb=" N ILE B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.667A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.966A pdb=" N ILE B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.715A pdb=" N SER B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 4.051A pdb=" N LEU B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 155 " --> pdb=" O PHE B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 155' Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.889A pdb=" N LEU C 12 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 removed outlier: 4.782A pdb=" N ARG C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N HIS C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 removed outlier: 3.515A pdb=" N SER C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.757A pdb=" N GLY C 159 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.660A 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: 3.991A pdb=" N TYR D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 84 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 124 removed outlier: 3.589A pdb=" N GLN D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 190 through 194 Processing helix chain 'D' and resid 199 through 209 removed outlier: 4.015A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.883A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 141 Processing helix chain 'E' and resid 144 through 153 Processing helix chain 'F' and resid 15 through 33 removed outlier: 3.647A pdb=" N TYR F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 71 through 80 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 57 through 68 removed outlier: 4.218A pdb=" N VAL G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.521A pdb=" N GLN G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 145 Processing helix chain 'G' and resid 148 through 154 removed outlier: 4.278A pdb=" N HIS G 153 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR G 154 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.636A pdb=" N VAL H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.503A pdb=" N ILE H 100 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'I' and resid 32 through 37 removed outlier: 3.636A pdb=" N PHE I 37 " --> pdb=" O PHE I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'I' and resid 47 through 52 removed outlier: 3.704A pdb=" N ARG I 51 " --> pdb=" O LEU I 47 " (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 removed outlier: 3.563A pdb=" N LEU J 16 " --> pdb=" O ASP J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'K' and resid 44 through 49 removed outlier: 4.007A pdb=" N ILE K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 56 removed outlier: 3.855A pdb=" N ARG K 54 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 55 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 74 removed outlier: 3.662A pdb=" N ALA K 61 " --> pdb=" O THR K 57 " (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 10 Processing helix chain 'L' and resid 21 through 25 removed outlier: 3.571A pdb=" N LEU L 24 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 20 removed outlier: 3.535A pdb=" N THR M 20 " --> pdb=" O ASP M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.641A pdb=" N TRP M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 16 through 20 removed outlier: 3.515A pdb=" N ARG N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.577A pdb=" N ARG O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 4.413A 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 removed outlier: 3.633A pdb=" N ARG P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 94 removed outlier: 4.223A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.790A pdb=" N SER Q 99 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 26 removed outlier: 3.610A pdb=" N LEU R 26 " --> pdb=" O LYS R 23 " (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 77 Processing helix chain 'S' and resid 12 through 24 removed outlier: 4.613A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.635A pdb=" N ARG T 17 " --> pdb=" O LEU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 69 removed outlier: 3.780A pdb=" N ALA T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 4.051A 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 45 Processing helix chain 'U' and resid 60 through 70 Processing helix chain 'U' and resid 79 through 84 Proline residue: U 84 - end of helix Processing helix chain 'U' and resid 85 through 90 removed outlier: 3.558A pdb=" N THR U 89 " --> pdb=" O ILE U 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 116 removed outlier: 4.149A pdb=" N VAL U 111 " --> pdb=" O ASP U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 143 removed outlier: 3.711A pdb=" N ILE U 136 " --> pdb=" O VAL U 132 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU U 141 " --> pdb=" O ILE U 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 181 Processing helix chain 'U' and resid 220 through 232 removed outlier: 3.589A pdb=" N PHE U 232 " --> pdb=" O ILE U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 247 Processing helix chain 'U' and resid 253 through 264 Processing helix chain 'U' and resid 271 through 275 Processing helix chain 'U' and resid 276 through 289 Processing helix chain 'V' and resid 8 through 16 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.310A pdb=" N PHE B 17 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 42 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS B 19 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 34 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 7.929A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 69 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 186 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 22 removed outlier: 4.112A pdb=" N ARG C 59 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS C 69 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR C 67 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.060A 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: 5.466A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 12 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.608A pdb=" N ILE E 118 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 37 through 52 removed outlier: 16.401A pdb=" N VAL F 40 " --> pdb=" O MET F 67 " (cutoff:3.500A) removed outlier: 16.424A pdb=" N MET F 67 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 15.268A pdb=" N GLU F 42 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 15.423A pdb=" N VAL F 65 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 13.597A pdb=" N GLY F 44 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N TYR F 63 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N ARG F 46 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N LEU F 61 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N LEU F 48 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N TYR F 59 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N TYR F 50 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLN F 57 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ARG F 3 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS F 92 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU F 5 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN F 7 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL F 88 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 74 through 79 Processing sheet with id=AB1, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB2, first strand: chain 'H' and resid 94 through 95 removed outlier: 6.051A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.509A pdb=" N ARG I 10 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'J' and resid 40 through 49 removed outlier: 4.490A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR J 42 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR J 67 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL J 44 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU J 65 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG J 46 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE J 63 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR J 48 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU J 61 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU J 8 " --> pdb=" O ARG J 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 40 through 49 removed outlier: 4.490A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR J 42 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR J 67 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL J 44 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU J 65 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG J 46 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE J 63 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR J 48 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU J 61 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.901A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLY K 17 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE K 83 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.536A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL L 36 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE L 97 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR L 66 " --> pdb=" O ILE L 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 49 through 51 removed outlier: 6.634A pdb=" N ILE P 19 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR P 17 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL P 2 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 5 through 15 removed outlier: 14.742A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.852A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL Q 9 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP Q 13 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR Q 18 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N LYS Q 69 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU Q 43 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 31 through 33 removed outlier: 3.563A pdb=" N THR S 33 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 99 through 100 removed outlier: 3.683A pdb=" N ILE U 99 " --> pdb=" O ALA U 75 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL U 74 " --> pdb=" O VAL U 52 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET U 123 " --> pdb=" O GLY U 51 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE U 122 " --> pdb=" O GLY U 149 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N VAL U 151 " --> pdb=" O ILE U 122 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL U 124 " --> pdb=" O VAL U 151 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N MET U 153 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER U 203 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE U 189 " --> pdb=" O SER U 203 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL U 205 " --> pdb=" O VAL U 187 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE U 209 " --> pdb=" O GLU U 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU U 183 " --> pdb=" O ILE U 209 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1062 hydrogen bonds 1774 hydrogen bond angles 0 basepair planarities 398 basepair parallelities 675 stacking parallelities Total time for adding SS restraints: 48.59 Time building geometry restraints manager: 26.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8894 1.34 - 1.46: 23652 1.46 - 1.58: 19498 1.58 - 1.70: 2785 1.70 - 1.82: 96 Bond restraints: 54925 Sorted by residual: bond pdb=" C ARG D 36 " pdb=" N PRO D 37 " ideal model delta sigma weight residual 1.334 1.358 -0.024 8.40e-03 1.42e+04 8.51e+00 bond pdb=" O5' G A 672 " pdb=" C5' G A 672 " ideal model delta sigma weight residual 1.420 1.460 -0.040 1.50e-02 4.44e+03 6.97e+00 bond pdb=" N GLY U 27 " pdb=" CA GLY U 27 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+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 6.50e+00 bond pdb=" N GLY D 2 " pdb=" CA GLY D 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.37e+00 ... (remaining 54920 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.04: 8390 106.04 - 113.17: 28810 113.17 - 120.29: 24792 120.29 - 127.42: 16135 127.42 - 134.55: 2929 Bond angle restraints: 81056 Sorted by residual: angle pdb=" O3' U A 82 " pdb=" C3' U A 82 " pdb=" C2' U A 82 " ideal model delta sigma weight residual 109.50 123.08 -13.58 1.50e+00 4.44e-01 8.19e+01 angle pdb=" O3' C A 88 " pdb=" C3' C A 88 " pdb=" C2' C A 88 " ideal model delta sigma weight residual 109.50 120.50 -11.00 1.50e+00 4.44e-01 5.38e+01 angle pdb=" O3' A A1269 " pdb=" C3' A A1269 " pdb=" C2' A A1269 " ideal model delta sigma weight residual 109.50 119.39 -9.89 1.50e+00 4.44e-01 4.35e+01 angle pdb=" O3' A A 156 " pdb=" C3' A A 156 " pdb=" C2' A A 156 " ideal model delta sigma weight residual 113.70 122.22 -8.52 1.50e+00 4.44e-01 3.23e+01 angle pdb=" C4' A A1269 " pdb=" C3' A A1269 " pdb=" O3' A A1269 " ideal model delta sigma weight residual 109.40 117.45 -8.05 1.50e+00 4.44e-01 2.88e+01 ... (remaining 81051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 31287 35.94 - 71.88: 3614 71.88 - 107.83: 520 107.83 - 143.77: 17 143.77 - 179.71: 27 Dihedral angle restraints: 35465 sinusoidal: 27915 harmonic: 7550 Sorted by residual: dihedral pdb=" C5' A A1269 " pdb=" C4' A A1269 " pdb=" C3' A A1269 " pdb=" O3' A A1269 " ideal model delta sinusoidal sigma weight residual 147.00 73.21 73.79 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C5' C A 88 " pdb=" C4' C A 88 " pdb=" C3' C A 88 " pdb=" O3' C A 88 " ideal model delta sinusoidal sigma weight residual 147.00 75.81 71.19 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" O4' C A 20 " pdb=" C1' C A 20 " pdb=" N1 C A 20 " pdb=" C2 C A 20 " ideal model delta sinusoidal sigma weight residual -160.00 19.71 -179.71 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 35462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 8114 0.148 - 0.296: 1994 0.296 - 0.444: 20 0.444 - 0.592: 2 0.592 - 0.740: 3 Chirality restraints: 10133 Sorted by residual: chirality pdb=" C3' C A 88 " pdb=" C4' C A 88 " pdb=" O3' C A 88 " pdb=" C2' C A 88 " both_signs ideal model delta sigma weight residual False -2.74 -2.00 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C3' U A 82 " pdb=" C4' U A 82 " pdb=" O3' U A 82 " pdb=" C2' U A 82 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C3' A A1269 " pdb=" C4' A A1269 " pdb=" O3' A A1269 " pdb=" C2' A A1269 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 10130 not shown) Planarity restraints: 5108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1503 " 0.022 2.00e-02 2.50e+03 2.07e-02 1.29e+01 pdb=" N9 G A1503 " -0.015 2.00e-02 2.50e+03 pdb=" C8 G A1503 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G A1503 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A1503 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G A1503 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G A1503 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G A1503 " 0.046 2.00e-02 2.50e+03 pdb=" C2 G A1503 " -0.042 2.00e-02 2.50e+03 pdb=" N2 G A1503 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A1503 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A1503 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 619 " 0.003 2.00e-02 2.50e+03 2.01e-02 1.22e+01 pdb=" N9 G A 619 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G A 619 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 619 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 619 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 619 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G A 619 " 0.027 2.00e-02 2.50e+03 pdb=" N1 G A 619 " -0.046 2.00e-02 2.50e+03 pdb=" C2 G A 619 " 0.042 2.00e-02 2.50e+03 pdb=" N2 G A 619 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 619 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 619 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 864 " -0.006 2.00e-02 2.50e+03 2.00e-02 1.20e+01 pdb=" N9 G A 864 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G A 864 " 0.012 2.00e-02 2.50e+03 pdb=" N7 G A 864 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G A 864 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 864 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G A 864 " 0.025 2.00e-02 2.50e+03 pdb=" N1 G A 864 " -0.042 2.00e-02 2.50e+03 pdb=" C2 G A 864 " 0.042 2.00e-02 2.50e+03 pdb=" N2 G A 864 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A 864 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 864 " -0.004 2.00e-02 2.50e+03 ... (remaining 5105 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1463 2.65 - 3.21: 42179 3.21 - 3.77: 99949 3.77 - 4.34: 129093 4.34 - 4.90: 181157 Nonbonded interactions: 453841 Sorted by model distance: nonbonded pdb=" O ASN U 29 " pdb=" OD1 ASN U 29 " model vdw 2.085 3.040 nonbonded pdb=" O2' C A 208 " pdb=" O4' U A 209 " model vdw 2.125 2.440 nonbonded pdb=" ND2 ASN U 29 " pdb=" OH TYR U 130 " model vdw 2.246 2.520 nonbonded pdb=" O2' A A1269 " pdb=" O5' A A1270 " model vdw 2.249 2.440 nonbonded pdb=" O2' A A1232 " pdb=" O4' A A1233 " model vdw 2.270 2.440 ... (remaining 453836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.070 Extract box with map and model: 10.040 Check model and map are aligned: 0.710 Set scattering table: 0.440 Process input model: 178.590 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.150 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 54925 Z= 0.500 Angle : 1.207 13.576 81056 Z= 0.771 Chirality : 0.111 0.740 10133 Planarity : 0.004 0.021 5108 Dihedral : 24.274 179.710 30607 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.04 % Favored : 92.69 % Rotamer: Outliers : 0.63 % Allowed : 4.85 % Favored : 94.51 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2584 helix: 0.30 (0.15), residues: 994 sheet: -0.68 (0.25), residues: 431 loop : -1.81 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 167 HIS 0.007 0.002 HIS S 14 PHE 0.013 0.002 PHE U 292 TYR 0.014 0.002 TYR U 171 ARG 0.010 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 327 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7493 (tppt) REVERT: B 48 MET cc_start: 0.8555 (mmm) cc_final: 0.8323 (mmm) REVERT: D 33 MET cc_start: 0.7829 (mmm) cc_final: 0.7619 (mmm) REVERT: E 56 GLN cc_start: 0.8229 (mt0) cc_final: 0.8009 (mt0) REVERT: E 76 ILE cc_start: 0.9236 (mm) cc_final: 0.9009 (mt) REVERT: F 15 ASP cc_start: 0.7563 (p0) cc_final: 0.7294 (p0) REVERT: G 43 PHE cc_start: 0.7637 (t80) cc_final: 0.7421 (t80) REVERT: G 109 ASN cc_start: 0.7987 (m110) cc_final: 0.7755 (m110) REVERT: H 42 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8191 (mm-30) REVERT: J 3 LYS cc_start: 0.5155 (ptpt) cc_final: 0.4187 (ttmm) REVERT: J 79 ARG cc_start: 0.6727 (mmp80) cc_final: 0.6493 (mmp80) REVERT: J 90 LEU cc_start: 0.4945 (mp) cc_final: 0.4667 (mm) REVERT: J 95 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6297 (tm-30) REVERT: K 47 VAL cc_start: 0.7391 (t) cc_final: 0.7094 (p) REVERT: K 57 THR cc_start: 0.8085 (m) cc_final: 0.7298 (m) REVERT: K 81 ASP cc_start: 0.6973 (m-30) cc_final: 0.6372 (m-30) REVERT: K 93 GLN cc_start: 0.5299 (pp30) cc_final: 0.4960 (pp30) REVERT: M 4 ILE cc_start: 0.4903 (mm) cc_final: 0.4660 (mt) REVERT: M 21 TYR cc_start: 0.6724 (m-80) cc_final: 0.6476 (m-10) REVERT: N 46 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7620 (mt-10) REVERT: Q 48 GLU cc_start: 0.8350 (mp0) cc_final: 0.8107 (mp0) REVERT: R 21 LYS cc_start: 0.7992 (mttm) cc_final: 0.7737 (mttm) REVERT: S 43 GLU cc_start: 0.7552 (mp0) cc_final: 0.7155 (tm-30) REVERT: S 66 MET cc_start: 0.4410 (ptt) cc_final: 0.4082 (ptt) REVERT: T 90 GLN cc_start: 0.8435 (mp10) cc_final: 0.7777 (mp10) REVERT: U 181 TYR cc_start: 0.7144 (m-10) cc_final: 0.6943 (m-10) REVERT: U 207 ARG cc_start: 0.6067 (ttp-110) cc_final: 0.5681 (ptm160) outliers start: 14 outliers final: 5 residues processed: 341 average time/residue: 0.7070 time to fit residues: 388.4744 Evaluate side-chains 242 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain T residue 100 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 200 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 186 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 355 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN C 6 HIS ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 HIS U 29 ASN U 144 HIS U 220 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 54925 Z= 0.143 Angle : 0.589 8.449 81056 Z= 0.303 Chirality : 0.036 0.311 10133 Planarity : 0.004 0.046 5108 Dihedral : 24.917 179.303 25165 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 1.13 % Allowed : 9.98 % Favored : 88.89 % 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: -0.42 (0.16), residues: 2584 helix: 1.08 (0.16), residues: 1022 sheet: -0.33 (0.25), residues: 461 loop : -1.57 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.009 0.001 HIS U 144 PHE 0.010 0.001 PHE H 31 TYR 0.026 0.001 TYR U 131 ARG 0.004 0.000 ARG K 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 264 time to evaluate : 4.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7479 (tppt) REVERT: C 142 MET cc_start: 0.7562 (mmm) cc_final: 0.7277 (mmt) REVERT: E 56 GLN cc_start: 0.8301 (mt0) cc_final: 0.8099 (mt0) REVERT: E 76 ILE cc_start: 0.9159 (mm) cc_final: 0.8901 (mt) REVERT: F 55 ASP cc_start: 0.7169 (m-30) cc_final: 0.6924 (t0) REVERT: G 15 ASP cc_start: 0.5844 (t0) cc_final: 0.5615 (m-30) REVERT: G 31 MET cc_start: 0.7076 (tmm) cc_final: 0.5979 (tmm) REVERT: G 73 MET cc_start: 0.6544 (tpp) cc_final: 0.6333 (tpp) REVERT: J 95 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6541 (tm-30) REVERT: K 50 TYR cc_start: 0.6908 (m-10) cc_final: 0.6603 (m-10) REVERT: K 81 ASP cc_start: 0.6998 (m-30) cc_final: 0.6597 (m-30) REVERT: P 34 GLU cc_start: 0.8531 (tt0) cc_final: 0.8166 (tt0) REVERT: R 21 LYS cc_start: 0.7813 (mttm) cc_final: 0.7596 (mttm) REVERT: R 84 LYS cc_start: 0.8092 (ptpt) cc_final: 0.7741 (mmmt) REVERT: S 43 GLU cc_start: 0.7518 (mp0) cc_final: 0.6891 (tm-30) REVERT: T 90 GLN cc_start: 0.8327 (mp10) cc_final: 0.7857 (tm-30) REVERT: U 52 VAL cc_start: 0.2928 (OUTLIER) cc_final: 0.2503 (p) REVERT: U 123 MET cc_start: 0.3336 (tmm) cc_final: 0.2798 (tmm) REVERT: U 198 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6305 (mm-40) REVERT: U 207 ARG cc_start: 0.5818 (ttp-110) cc_final: 0.5552 (ptm160) outliers start: 25 outliers final: 10 residues processed: 284 average time/residue: 0.6602 time to fit residues: 310.9579 Evaluate side-chains 242 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 230 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 198 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 296 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 356 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 chunk 317 optimal weight: 8.9990 chunk 353 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 286 optimal weight: 0.2980 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN O 37 ASN U 29 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 54925 Z= 0.263 Angle : 0.613 8.344 81056 Z= 0.314 Chirality : 0.038 0.304 10133 Planarity : 0.005 0.054 5108 Dihedral : 24.852 179.661 25164 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.77 % Rotamer: Outliers : 2.13 % Allowed : 12.43 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2584 helix: 1.12 (0.16), residues: 1024 sheet: -0.42 (0.25), residues: 460 loop : -1.48 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 138 HIS 0.004 0.001 HIS J 56 PHE 0.010 0.001 PHE U 30 TYR 0.025 0.002 TYR M 21 ARG 0.008 0.001 ARG O 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7651 (tppt) REVERT: B 143 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: E 76 ILE cc_start: 0.9213 (mm) cc_final: 0.8994 (mt) REVERT: G 15 ASP cc_start: 0.5941 (t0) cc_final: 0.5646 (m-30) REVERT: G 73 MET cc_start: 0.6460 (tpp) cc_final: 0.6222 (tpp) REVERT: J 3 LYS cc_start: 0.5673 (tppt) cc_final: 0.4981 (ttmm) REVERT: K 77 MET cc_start: 0.6203 (mmp) cc_final: 0.5909 (mmm) REVERT: K 81 ASP cc_start: 0.6740 (m-30) cc_final: 0.6299 (m-30) REVERT: M 3 ARG cc_start: 0.4339 (mmm160) cc_final: 0.3781 (mmp-170) REVERT: P 47 ASP cc_start: 0.8546 (p0) cc_final: 0.8283 (p0) REVERT: R 21 LYS cc_start: 0.7842 (mttm) cc_final: 0.7581 (mttm) REVERT: S 43 GLU cc_start: 0.7479 (mp0) cc_final: 0.6656 (tm-30) REVERT: T 90 GLN cc_start: 0.8110 (mp10) cc_final: 0.7768 (tm-30) REVERT: U 52 VAL cc_start: 0.2993 (OUTLIER) cc_final: 0.2599 (p) REVERT: U 123 MET cc_start: 0.3511 (tmm) cc_final: 0.3010 (tmm) REVERT: U 181 TYR cc_start: 0.7028 (m-10) cc_final: 0.6515 (m-10) REVERT: U 198 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6295 (mm-40) outliers start: 47 outliers final: 27 residues processed: 262 average time/residue: 0.6398 time to fit residues: 280.8568 Evaluate side-chains 243 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 198 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 378 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 339 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54925 Z= 0.249 Angle : 0.604 8.325 81056 Z= 0.309 Chirality : 0.037 0.264 10133 Planarity : 0.005 0.056 5108 Dihedral : 24.825 179.970 25164 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.00 % Favored : 93.89 % Rotamer: Outliers : 2.22 % Allowed : 13.79 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2584 helix: 1.18 (0.16), residues: 1019 sheet: -0.39 (0.25), residues: 449 loop : -1.49 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 138 HIS 0.004 0.001 HIS J 56 PHE 0.010 0.001 PHE H 31 TYR 0.019 0.002 TYR U 131 ARG 0.007 0.000 ARG O 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 217 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7670 (tppt) REVERT: B 143 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8076 (mm-30) REVERT: E 76 ILE cc_start: 0.9287 (mm) cc_final: 0.9040 (mt) REVERT: G 15 ASP cc_start: 0.5833 (t0) cc_final: 0.5564 (m-30) REVERT: G 105 VAL cc_start: 0.7559 (t) cc_final: 0.7203 (m) REVERT: G 144 MET cc_start: 0.7699 (mmp) cc_final: 0.7466 (mmp) REVERT: J 95 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6299 (tm-30) REVERT: K 77 MET cc_start: 0.6141 (mmp) cc_final: 0.5858 (mmm) REVERT: K 81 ASP cc_start: 0.6707 (m-30) cc_final: 0.6311 (m-30) REVERT: K 87 THR cc_start: 0.8171 (t) cc_final: 0.7783 (p) REVERT: M 3 ARG cc_start: 0.4568 (mmm160) cc_final: 0.3505 (tmm160) REVERT: P 47 ASP cc_start: 0.8663 (p0) cc_final: 0.8334 (p0) REVERT: R 21 LYS cc_start: 0.7899 (mttm) cc_final: 0.7640 (mttm) REVERT: S 43 GLU cc_start: 0.7314 (mp0) cc_final: 0.6518 (tm-30) REVERT: T 90 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: U 52 VAL cc_start: 0.3013 (OUTLIER) cc_final: 0.2654 (p) REVERT: U 123 MET cc_start: 0.3583 (tmm) cc_final: 0.3142 (tmm) REVERT: U 181 TYR cc_start: 0.7161 (m-10) cc_final: 0.6688 (m-10) REVERT: U 198 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.6218 (mt0) outliers start: 49 outliers final: 32 residues processed: 253 average time/residue: 0.6289 time to fit residues: 269.0263 Evaluate side-chains 241 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 198 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 95 optimal weight: 30.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN G 68 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 54925 Z= 0.369 Angle : 0.694 8.525 81056 Z= 0.352 Chirality : 0.041 0.252 10133 Planarity : 0.006 0.059 5108 Dihedral : 24.900 178.890 25164 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 3.13 % Allowed : 14.97 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2584 helix: 0.92 (0.16), residues: 1029 sheet: -0.63 (0.25), residues: 435 loop : -1.56 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.016 0.002 PHE C 10 TYR 0.017 0.002 TYR D 138 ARG 0.007 0.001 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 213 time to evaluate : 3.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7556 (tppt) REVERT: B 143 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: C 6 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.6501 (t70) REVERT: C 17 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6356 (t0) REVERT: C 201 TYR cc_start: 0.6507 (m-80) cc_final: 0.6100 (m-80) REVERT: E 76 ILE cc_start: 0.9230 (mm) cc_final: 0.8944 (mt) REVERT: F 50 TYR cc_start: 0.8023 (p90) cc_final: 0.7668 (p90) REVERT: F 55 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6710 (t0) REVERT: G 105 VAL cc_start: 0.7560 (t) cc_final: 0.7211 (m) REVERT: J 95 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6311 (tm-30) REVERT: K 78 GLN cc_start: 0.7759 (mt0) cc_final: 0.7297 (pt0) REVERT: K 81 ASP cc_start: 0.6419 (m-30) cc_final: 0.6052 (m-30) REVERT: K 87 THR cc_start: 0.8305 (t) cc_final: 0.7839 (p) REVERT: K 103 LEU cc_start: 0.5867 (mt) cc_final: 0.4579 (mp) REVERT: M 3 ARG cc_start: 0.4338 (mmm160) cc_final: 0.3682 (tmm160) REVERT: O 6 GLU cc_start: 0.8659 (mp0) cc_final: 0.8451 (mp0) REVERT: O 74 ASP cc_start: 0.8007 (t0) cc_final: 0.7799 (t0) REVERT: R 21 LYS cc_start: 0.7923 (mttm) cc_final: 0.7592 (mttm) REVERT: S 43 GLU cc_start: 0.7408 (mp0) cc_final: 0.6483 (tm-30) REVERT: T 90 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: U 65 GLN cc_start: 0.5955 (OUTLIER) cc_final: 0.5689 (mp10) REVERT: U 123 MET cc_start: 0.3569 (tmm) cc_final: 0.3150 (tmm) REVERT: U 153 MET cc_start: 0.8145 (ppp) cc_final: 0.7831 (ppp) REVERT: U 181 TYR cc_start: 0.7405 (m-10) cc_final: 0.7201 (m-10) REVERT: U 198 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6400 (mt0) outliers start: 69 outliers final: 43 residues processed: 267 average time/residue: 0.6159 time to fit residues: 278.3012 Evaluate side-chains 253 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 198 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 30.0000 chunk 341 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 379 optimal weight: 0.0980 chunk 314 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 overall best weight: 6.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN E 56 GLN G 68 ASN U 29 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 54925 Z= 0.380 Angle : 0.701 8.329 81056 Z= 0.355 Chirality : 0.041 0.250 10133 Planarity : 0.006 0.056 5108 Dihedral : 24.926 179.687 25164 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 3.22 % Allowed : 16.28 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2584 helix: 0.72 (0.16), residues: 1037 sheet: -0.74 (0.25), residues: 432 loop : -1.63 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.014 0.002 PHE G 62 TYR 0.017 0.002 TYR D 138 ARG 0.006 0.001 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 210 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7841 (tptt) REVERT: B 48 MET cc_start: 0.8444 (mmm) cc_final: 0.8171 (mmm) REVERT: B 55 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: B 143 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: C 201 TYR cc_start: 0.6505 (m-80) cc_final: 0.6066 (m-80) REVERT: E 76 ILE cc_start: 0.9177 (mm) cc_final: 0.8961 (mt) REVERT: F 50 TYR cc_start: 0.8065 (p90) cc_final: 0.7704 (p90) REVERT: G 105 VAL cc_start: 0.7545 (t) cc_final: 0.7201 (m) REVERT: J 95 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6291 (tm-30) REVERT: K 81 ASP cc_start: 0.6433 (m-30) cc_final: 0.6118 (m-30) REVERT: K 103 LEU cc_start: 0.5796 (mt) cc_final: 0.4557 (mp) REVERT: M 3 ARG cc_start: 0.3988 (mmm160) cc_final: 0.3257 (ttp80) REVERT: N 46 GLU cc_start: 0.8056 (mt-10) cc_final: 0.6814 (mp0) REVERT: O 6 GLU cc_start: 0.8687 (mp0) cc_final: 0.8454 (mp0) REVERT: R 21 LYS cc_start: 0.8185 (mttm) cc_final: 0.7887 (mttm) REVERT: S 43 GLU cc_start: 0.7407 (mp0) cc_final: 0.6455 (tm-30) REVERT: T 90 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: U 65 GLN cc_start: 0.5859 (OUTLIER) cc_final: 0.5573 (mp10) REVERT: U 198 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6314 (mt0) outliers start: 71 outliers final: 52 residues processed: 267 average time/residue: 0.6430 time to fit residues: 287.6382 Evaluate side-chains 254 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 197 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 122 HIS Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 377 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 GLN ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 54925 Z= 0.288 Angle : 0.644 8.615 81056 Z= 0.328 Chirality : 0.039 0.246 10133 Planarity : 0.005 0.055 5108 Dihedral : 24.890 179.416 25164 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 3.36 % Allowed : 16.37 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2584 helix: 0.90 (0.16), residues: 1037 sheet: -0.69 (0.25), residues: 431 loop : -1.54 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.012 0.002 PHE C 10 TYR 0.017 0.002 TYR U 131 ARG 0.005 0.001 ARG T 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 203 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7702 (tppt) REVERT: B 55 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7562 (m-10) REVERT: B 143 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: C 6 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.6246 (t70) REVERT: C 17 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6339 (t0) REVERT: C 201 TYR cc_start: 0.6445 (m-80) cc_final: 0.6057 (m-80) REVERT: E 76 ILE cc_start: 0.9252 (mm) cc_final: 0.8985 (mt) REVERT: F 23 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8422 (mttm) REVERT: F 50 TYR cc_start: 0.8070 (p90) cc_final: 0.7715 (p90) REVERT: F 55 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6688 (t0) REVERT: G 105 VAL cc_start: 0.7510 (t) cc_final: 0.7167 (m) REVERT: J 95 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6278 (tm-30) REVERT: K 81 ASP cc_start: 0.6582 (m-30) cc_final: 0.6279 (m-30) REVERT: M 20 THR cc_start: 0.7392 (t) cc_final: 0.7151 (p) REVERT: N 8 GLU cc_start: 0.5178 (OUTLIER) cc_final: 0.4130 (tm-30) REVERT: N 46 GLU cc_start: 0.7987 (mt-10) cc_final: 0.6854 (mp0) REVERT: O 6 GLU cc_start: 0.8723 (mp0) cc_final: 0.8490 (mp0) REVERT: P 34 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: R 21 LYS cc_start: 0.8153 (mttm) cc_final: 0.7854 (mttm) REVERT: S 66 MET cc_start: 0.3928 (OUTLIER) cc_final: 0.3550 (mtm) REVERT: T 90 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: U 65 GLN cc_start: 0.6073 (OUTLIER) cc_final: 0.5719 (mp10) REVERT: U 198 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.6320 (mt0) outliers start: 74 outliers final: 51 residues processed: 261 average time/residue: 0.6488 time to fit residues: 285.1773 Evaluate side-chains 257 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 195 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 195 PHE Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 240 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 GLN ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 54925 Z= 0.303 Angle : 0.653 8.741 81056 Z= 0.332 Chirality : 0.039 0.254 10133 Planarity : 0.005 0.055 5108 Dihedral : 24.869 179.932 25160 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 3.45 % Allowed : 17.10 % Favored : 79.46 % 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: -0.59 (0.17), residues: 2584 helix: 0.92 (0.16), residues: 1025 sheet: -0.71 (0.25), residues: 431 loop : -1.48 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 138 HIS 0.010 0.001 HIS G 122 PHE 0.010 0.002 PHE D 79 TYR 0.026 0.002 TYR K 50 ARG 0.008 0.001 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 204 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7813 (tptt) REVERT: B 55 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7566 (m-10) REVERT: B 143 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: C 6 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6244 (t70) REVERT: C 17 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6341 (t0) REVERT: C 62 ASP cc_start: 0.7523 (t0) cc_final: 0.7320 (t0) REVERT: C 201 TYR cc_start: 0.6453 (m-80) cc_final: 0.6068 (m-80) REVERT: E 76 ILE cc_start: 0.9154 (mm) cc_final: 0.8934 (mt) REVERT: F 23 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8370 (mttp) REVERT: F 50 TYR cc_start: 0.8061 (p90) cc_final: 0.7690 (p90) REVERT: F 55 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6682 (t0) REVERT: G 105 VAL cc_start: 0.7507 (t) cc_final: 0.7163 (m) REVERT: J 95 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6291 (tm-30) REVERT: K 73 MET cc_start: 0.7504 (mmm) cc_final: 0.7072 (mpp) REVERT: K 81 ASP cc_start: 0.6564 (m-30) cc_final: 0.6272 (m-30) REVERT: M 3 ARG cc_start: 0.3938 (mmp-170) cc_final: 0.3689 (tmm160) REVERT: N 8 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.4080 (tm-30) REVERT: N 46 GLU cc_start: 0.7946 (mt-10) cc_final: 0.6822 (mp0) REVERT: O 6 GLU cc_start: 0.8705 (mp0) cc_final: 0.8456 (mp0) REVERT: P 34 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: R 21 LYS cc_start: 0.8142 (mttm) cc_final: 0.7858 (mttm) REVERT: S 66 MET cc_start: 0.3920 (OUTLIER) cc_final: 0.3549 (mtm) REVERT: T 62 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8802 (mp) REVERT: T 90 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: U 65 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5957 (mp10) REVERT: U 153 MET cc_start: 0.7857 (ppp) cc_final: 0.6864 (ppp) REVERT: U 198 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6443 (mt0) outliers start: 76 outliers final: 56 residues processed: 265 average time/residue: 0.6291 time to fit residues: 279.4293 Evaluate side-chains 262 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 194 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 122 HIS Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.4980 chunk 361 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 352 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 318 optimal weight: 0.9980 chunk 332 optimal weight: 4.9990 chunk 350 optimal weight: 50.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN U 100 HIS ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54925 Z= 0.202 Angle : 0.593 10.951 81056 Z= 0.302 Chirality : 0.036 0.240 10133 Planarity : 0.004 0.054 5108 Dihedral : 24.807 178.961 25160 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.23 % Favored : 93.65 % Rotamer: Outliers : 2.68 % Allowed : 18.00 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2584 helix: 1.15 (0.16), residues: 1024 sheet: -0.63 (0.26), residues: 410 loop : -1.39 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.013 0.001 PHE G 62 TYR 0.019 0.001 TYR K 50 ARG 0.008 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 208 time to evaluate : 3.854 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 8 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7573 (tppt) REVERT: B 48 MET cc_start: 0.8553 (mmm) cc_final: 0.8269 (mmm) REVERT: B 55 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7536 (m-10) REVERT: B 143 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: C 6 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.6219 (t70) REVERT: C 201 TYR cc_start: 0.6397 (m-80) cc_final: 0.6016 (m-80) REVERT: D 190 ASP cc_start: 0.8141 (p0) cc_final: 0.7757 (p0) REVERT: E 76 ILE cc_start: 0.9228 (mm) cc_final: 0.8984 (mt) REVERT: F 23 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8525 (mttp) REVERT: F 50 TYR cc_start: 0.8008 (p90) cc_final: 0.7651 (p90) REVERT: G 31 MET cc_start: 0.7239 (tmm) cc_final: 0.6384 (tmm) REVERT: J 95 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6270 (tm-30) REVERT: K 77 MET cc_start: 0.6863 (mmm) cc_final: 0.6456 (mmp) REVERT: K 81 ASP cc_start: 0.6540 (m-30) cc_final: 0.6262 (m-30) REVERT: M 3 ARG cc_start: 0.4204 (mmp-170) cc_final: 0.3780 (tmm160) REVERT: O 6 GLU cc_start: 0.8728 (mp0) cc_final: 0.8499 (mp0) REVERT: P 34 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8262 (tp30) REVERT: R 21 LYS cc_start: 0.8146 (mttm) cc_final: 0.7865 (mttm) REVERT: S 66 MET cc_start: 0.3809 (OUTLIER) cc_final: 0.3466 (mtm) REVERT: T 62 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8817 (mp) REVERT: T 90 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: U 65 GLN cc_start: 0.6246 (OUTLIER) cc_final: 0.5812 (mp10) REVERT: U 153 MET cc_start: 0.7927 (ppp) cc_final: 0.7115 (ppp) REVERT: U 198 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.6431 (mt0) outliers start: 59 outliers final: 43 residues processed: 254 average time/residue: 0.6434 time to fit residues: 274.5167 Evaluate side-chains 249 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 195 PHE Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 30.0000 chunk 372 optimal weight: 0.8980 chunk 227 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 390 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN K 78 GLN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 54925 Z= 0.302 Angle : 0.647 10.991 81056 Z= 0.328 Chirality : 0.039 0.240 10133 Planarity : 0.005 0.054 5108 Dihedral : 24.807 179.739 25160 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.70 % Favored : 93.19 % Rotamer: Outliers : 2.90 % Allowed : 17.96 % Favored : 79.14 % 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: -0.44 (0.17), residues: 2584 helix: 1.06 (0.16), residues: 1018 sheet: -0.64 (0.26), residues: 414 loop : -1.39 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.010 0.002 PHE D 79 TYR 0.018 0.002 TYR K 50 ARG 0.010 0.001 ARG K 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 194 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7790 (tptt) REVERT: B 48 MET cc_start: 0.8541 (mmm) cc_final: 0.8225 (mmm) REVERT: B 55 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: B 143 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: C 6 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.6244 (t70) REVERT: C 17 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6317 (t0) REVERT: C 201 TYR cc_start: 0.6448 (m-80) cc_final: 0.6055 (m-80) REVERT: D 190 ASP cc_start: 0.7737 (p0) cc_final: 0.7389 (p0) REVERT: E 76 ILE cc_start: 0.9204 (mm) cc_final: 0.8964 (mt) REVERT: F 50 TYR cc_start: 0.8066 (p90) cc_final: 0.7658 (p90) REVERT: G 31 MET cc_start: 0.7216 (tmm) cc_final: 0.6714 (tmm) REVERT: J 95 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6486 (tm-30) REVERT: K 81 ASP cc_start: 0.6494 (m-30) cc_final: 0.6227 (m-30) REVERT: M 3 ARG cc_start: 0.4025 (mmp-170) cc_final: 0.3708 (tmm160) REVERT: M 31 LYS cc_start: 0.8071 (pttp) cc_final: 0.7859 (ptpp) REVERT: N 8 GLU cc_start: 0.5232 (OUTLIER) cc_final: 0.4164 (tm-30) REVERT: O 6 GLU cc_start: 0.8722 (mp0) cc_final: 0.8471 (mp0) REVERT: P 34 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: S 66 MET cc_start: 0.3824 (OUTLIER) cc_final: 0.3478 (mtm) REVERT: T 62 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8830 (mp) REVERT: T 90 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: U 65 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5960 (mp10) REVERT: U 153 MET cc_start: 0.7860 (ppp) cc_final: 0.6831 (ppp) REVERT: U 198 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6387 (mt0) outliers start: 64 outliers final: 51 residues processed: 243 average time/residue: 0.6326 time to fit residues: 260.5853 Evaluate side-chains 254 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 192 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 122 HIS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 4.9990 chunk 331 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 286 optimal weight: 0.0040 chunk 45 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 319 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.058541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.041977 restraints weight = 264664.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.042777 restraints weight = 141054.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.042424 restraints weight = 100644.885| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 54925 Z= 0.289 Angle : 0.644 10.710 81056 Z= 0.327 Chirality : 0.038 0.238 10133 Planarity : 0.005 0.054 5108 Dihedral : 24.811 179.505 25160 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 3.27 % Allowed : 17.91 % Favored : 78.82 % 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: -0.46 (0.17), residues: 2584 helix: 1.06 (0.16), residues: 1018 sheet: -0.65 (0.26), residues: 414 loop : -1.42 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.010 0.001 PHE D 79 TYR 0.023 0.002 TYR K 50 ARG 0.015 0.001 ARG G 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7086.24 seconds wall clock time: 133 minutes 42.90 seconds (8022.90 seconds total)