Starting phenix.real_space_refine on Sun Feb 25 11:05:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2p_31659/02_2024/7v2p_31659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2p_31659/02_2024/7v2p_31659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2p_31659/02_2024/7v2p_31659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2p_31659/02_2024/7v2p_31659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2p_31659/02_2024/7v2p_31659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2p_31659/02_2024/7v2p_31659.pdb" } resolution = 3.3 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= 0.015 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 26691 2.51 5 N 9617 2.21 5 O 13376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q GLU 86": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 38": "OE1" <-> "OE2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "U GLU 45": "OE1" <-> "OE2" Residue "U GLU 249": "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: 51135 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': 119, 'rna2p_pyr': 93, 'rna3p_pur': 671, 'rna3p_pyr': 511} Link IDs: {'rna2p': 212, 'rna3p': 1181} 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: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2203 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 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 91.165 73.511 88.459 1.00 54.05 S ATOM 33460 SG CYS D 12 92.486 76.306 91.260 1.00 54.64 S ATOM 33578 SG CYS D 26 94.344 72.276 89.586 1.00 58.25 S ATOM 33618 SG CYS D 31 95.481 74.957 88.319 1.00 60.42 S ATOM 44196 SG CYS N 24 65.934 120.027 47.764 1.00 46.61 S ATOM 44220 SG CYS N 27 64.413 118.658 50.822 1.00 45.75 S ATOM 44327 SG CYS N 40 65.197 122.542 50.610 1.00 43.89 S ATOM 44352 SG CYS N 43 68.029 120.267 50.855 1.00 44.15 S Time building chain proxies: 26.72, per 1000 atoms: 0.52 Number of scatterers: 51135 At special positions: 0 Unit cell: (143.52, 215.28, 219.42, 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 13376 8.00 N 9617 7.00 C 26691 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: 25.96 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 12 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 12 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4884 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 23 sheets defined 44.0% alpha, 18.5% beta 481 base pairs and 726 stacking pairs defined. Time for finding SS restraints: 22.74 Creating SS restraints... Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.706A pdb=" N GLY B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.495A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 65 removed outlier: 3.663A pdb=" N THR B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.612A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 6.730A pdb=" N GLU B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 129 " --> pdb=" O GLU B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 129' Processing helix chain 'B' and resid 131 through 150 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.533A pdb=" N LEU C 12 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.899A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.594A pdb=" N GLY C 159 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.733A 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 98 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 113 through 123 removed outlier: 3.867A pdb=" N GLN D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 153 removed outlier: 3.637A pdb=" N ARG D 153 " --> pdb=" O GLU D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 150 through 153' Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.596A pdb=" N ALA D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 4.058A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.596A 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: 3.618A 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 20 through 31 removed outlier: 3.843A pdb=" N THR G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.818A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 removed outlier: 3.544A pdb=" N VAL G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 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 152 removed outlier: 3.572A pdb=" N TYR G 151 " --> pdb=" O ASN G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.669A pdb=" N VAL H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 removed outlier: 3.566A pdb=" N GLU H 42 " --> pdb=" O ILE H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'I' and resid 33 through 37 Processing helix chain 'I' and resid 40 through 46 removed outlier: 3.572A pdb=" N ALA I 43 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL I 44 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 52 Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'J' and resid 13 through 30 Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'K' and resid 45 through 49 removed outlier: 3.792A pdb=" N GLY K 49 " --> pdb=" O GLY K 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 49' Processing helix chain 'K' and resid 51 through 56 removed outlier: 3.679A pdb=" N ARG K 54 " --> pdb=" O LYS K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 75 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 Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 44 through 48 removed outlier: 3.513A pdb=" N LEU M 48 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.571A pdb=" N TRP M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.665A pdb=" N LEU M 70 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.565A pdb=" N HIS O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'Q' and resid 81 through 94 removed outlier: 4.440A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 98 Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 42 through 44 No H-bonds generated for 'chain 'R' and resid 42 through 44' Processing helix chain 'R' and resid 52 through 57 Processing helix chain 'R' and resid 59 through 76 Processing helix chain 'S' and resid 12 through 24 removed outlier: 3.815A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 removed outlier: 3.931A pdb=" N VAL S 45 " --> pdb=" O PRO S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 67 removed outlier: 3.573A pdb=" N MET S 66 " --> pdb=" O THR S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.540A pdb=" N ARG T 17 " --> pdb=" O LEU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 69 removed outlier: 3.848A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 93 removed outlier: 3.677A pdb=" N ARG T 89 " --> pdb=" O MET T 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 17 removed outlier: 4.072A pdb=" N LYS U 12 " --> pdb=" O PRO U 8 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU U 13 " --> pdb=" O ILE U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 45 removed outlier: 3.576A pdb=" N ASN U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL U 41 " --> pdb=" O LEU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 68 removed outlier: 4.094A pdb=" N GLN U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 90 removed outlier: 4.127A pdb=" N LYS U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP U 88 " --> pdb=" O PRO U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 115 removed outlier: 3.621A pdb=" N VAL U 111 " --> pdb=" O ASP U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 129 through 143 removed outlier: 3.978A pdb=" N THR U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) Proline residue: U 135 - end of helix Processing helix chain 'U' and resid 155 through 164 removed outlier: 3.524A pdb=" N ALA U 159 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG U 161 " --> pdb=" O GLU U 157 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 181 Processing helix chain 'U' and resid 220 through 232 removed outlier: 3.522A 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 removed outlier: 3.619A pdb=" N GLU U 262 " --> pdb=" O GLU U 258 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 275 Processing helix chain 'U' and resid 276 through 288 Processing helix chain 'V' and resid 8 through 16 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20 removed outlier: 5.942A pdb=" N PHE B 17 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 42 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS B 19 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 34 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 8.132A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 69 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE B 162 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 184 " --> pdb=" O TYR B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 21 removed outlier: 3.582A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.945A pdb=" N ASP D 144 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 6.746A pdb=" N LEU E 31 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE E 13 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY E 29 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG E 15 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG E 27 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA E 17 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG E 25 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET E 19 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY E 23 " --> pdb=" O MET E 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 52 removed outlier: 6.927A pdb=" N GLU F 38 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N GLU F 66 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL F 40 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN F 64 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU F 42 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TRP F 62 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F 58 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.981A pdb=" N ALA F 99 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE R 29 " --> pdb=" O ALA F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 73 through 80 Processing sheet with id=AB2, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB3, first strand: chain 'H' and resid 83 through 85 removed outlier: 3.719A pdb=" N GLU H 136 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 83 through 85 removed outlier: 3.719A pdb=" N GLU H 136 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE H 111 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU H 136 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE H 109 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'J' and resid 38 through 49 removed outlier: 6.920A pdb=" N LEU J 71 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 38 through 49 removed outlier: 6.920A pdb=" N LEU J 71 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 39 through 44 removed outlier: 5.947A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.594A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL L 36 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 49 through 51 removed outlier: 6.579A pdb=" N ILE P 19 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR P 17 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL P 2 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 5 through 15 removed outlier: 14.743A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Q 9 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP Q 13 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR Q 18 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 31 through 33 Processing sheet with id=AC5, first strand: chain 'U' and resid 96 through 99 removed outlier: 6.706A pdb=" N VAL U 73 " --> pdb=" O THR U 97 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE U 99 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA U 75 " --> pdb=" O ILE U 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE U 53 " --> pdb=" O MET U 123 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE U 122 " --> pdb=" O GLY U 149 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N VAL U 151 " --> pdb=" O ILE U 122 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL U 124 " --> pdb=" O VAL U 151 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N MET U 153 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA U 126 " --> pdb=" O MET U 153 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER U 203 " --> pdb=" O VAL U 190 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG U 207 " --> pdb=" O THR U 186 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR U 186 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE U 209 " --> pdb=" O ALA U 184 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA U 184 " --> pdb=" O ILE U 209 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1268 hydrogen bonds 2058 hydrogen bond angles 0 basepair planarities 481 basepair parallelities 726 stacking parallelities Total time for adding SS restraints: 46.81 Time building geometry restraints manager: 27.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6482 1.33 - 1.45: 23223 1.45 - 1.58: 22456 1.58 - 1.70: 2785 1.70 - 1.82: 96 Bond restraints: 55042 Sorted by residual: bond pdb=" C GLN U 198 " pdb=" N PRO U 199 " ideal model delta sigma weight residual 1.331 1.355 -0.024 7.90e-03 1.60e+04 9.20e+00 bond pdb=" C LEU U 247 " pdb=" N PRO U 248 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.27e-02 6.20e+03 6.90e+00 bond pdb=" C SER B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 6.89e+00 bond pdb=" C VAL U 196 " pdb=" N PRO U 197 " ideal model delta sigma weight residual 1.335 1.358 -0.023 8.70e-03 1.32e+04 6.83e+00 bond pdb=" C ARG D 36 " pdb=" N PRO D 37 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.25e+00 ... (remaining 55037 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.53: 6737 105.53 - 112.77: 30032 112.77 - 120.02: 23251 120.02 - 127.26: 17875 127.26 - 134.51: 3316 Bond angle restraints: 81211 Sorted by residual: angle pdb=" O3' U A 970 " pdb=" C3' U A 970 " pdb=" C2' U A 970 " ideal model delta sigma weight residual 109.50 119.09 -9.59 1.50e+00 4.44e-01 4.09e+01 angle pdb=" C4' U A 862 " pdb=" C3' U A 862 " pdb=" O3' U A 862 " ideal model delta sigma weight residual 109.40 118.92 -9.52 1.50e+00 4.44e-01 4.03e+01 angle pdb=" C4' G A1036 " pdb=" C3' G A1036 " pdb=" O3' G A1036 " ideal model delta sigma weight residual 109.40 118.86 -9.46 1.50e+00 4.44e-01 3.98e+01 angle pdb=" O3' G A1036 " pdb=" C3' G A1036 " pdb=" C2' G A1036 " ideal model delta sigma weight residual 109.50 118.94 -9.44 1.50e+00 4.44e-01 3.96e+01 angle pdb=" C4' A A 979 " pdb=" C3' A A 979 " pdb=" O3' A A 979 " ideal model delta sigma weight residual 109.40 118.47 -9.07 1.50e+00 4.44e-01 3.66e+01 ... (remaining 81206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 31677 35.72 - 71.45: 3362 71.45 - 107.17: 479 107.17 - 142.89: 7 142.89 - 178.62: 14 Dihedral angle restraints: 35539 sinusoidal: 27950 harmonic: 7589 Sorted by residual: dihedral pdb=" C5' U A1118 " pdb=" C4' U A1118 " pdb=" C3' U A1118 " pdb=" O3' U A1118 " ideal model delta sinusoidal sigma weight residual 147.00 82.96 64.04 1 8.00e+00 1.56e-02 8.43e+01 dihedral pdb=" O4' U A 361 " pdb=" C1' U A 361 " pdb=" N1 U A 361 " pdb=" C2 U A 361 " ideal model delta sinusoidal sigma weight residual 200.00 51.47 148.53 1 1.50e+01 4.44e-03 7.91e+01 dihedral pdb=" C4' U A1118 " pdb=" C3' U A1118 " pdb=" C2' U A1118 " pdb=" C1' U A1118 " ideal model delta sinusoidal sigma weight residual -35.00 25.46 -60.46 1 8.00e+00 1.56e-02 7.60e+01 ... (remaining 35536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 8910 0.150 - 0.301: 1228 0.301 - 0.451: 8 0.451 - 0.601: 2 0.601 - 0.752: 3 Chirality restraints: 10151 Sorted by residual: chirality pdb=" C3' G A1036 " pdb=" C4' G A1036 " pdb=" O3' G A1036 " pdb=" C2' G A1036 " both_signs ideal model delta sigma weight residual False -2.74 -1.99 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C3' A A 979 " pdb=" C4' A A 979 " pdb=" O3' A A 979 " pdb=" C2' A A 979 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.61 2.00e-01 2.50e+01 9.36e+00 chirality pdb=" C3' U A 970 " pdb=" C4' U A 970 " pdb=" O3' U A 970 " pdb=" C2' U A 970 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.04e+00 ... (remaining 10148 not shown) Planarity restraints: 5125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 577 " 0.004 2.00e-02 2.50e+03 1.83e-02 1.00e+01 pdb=" N9 G A 577 " -0.000 2.00e-02 2.50e+03 pdb=" C8 G A 577 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G A 577 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 577 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 577 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G A 577 " 0.023 2.00e-02 2.50e+03 pdb=" N1 G A 577 " -0.045 2.00e-02 2.50e+03 pdb=" C2 G A 577 " 0.035 2.00e-02 2.50e+03 pdb=" N2 G A 577 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 577 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 577 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1503 " -0.004 2.00e-02 2.50e+03 1.74e-02 9.13e+00 pdb=" N9 G A1503 " -0.005 2.00e-02 2.50e+03 pdb=" C8 G A1503 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G A1503 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G A1503 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A1503 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G A1503 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G A1503 " -0.042 2.00e-02 2.50e+03 pdb=" C2 G A1503 " 0.038 2.00e-02 2.50e+03 pdb=" N2 G A1503 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G A1503 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G A1503 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 23 " -0.000 2.00e-02 2.50e+03 1.54e-02 7.08e+00 pdb=" N9 G A 23 " -0.001 2.00e-02 2.50e+03 pdb=" C8 G A 23 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 23 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 23 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 23 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G A 23 " 0.025 2.00e-02 2.50e+03 pdb=" N1 G A 23 " -0.034 2.00e-02 2.50e+03 pdb=" C2 G A 23 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G A 23 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 23 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G A 23 " 0.003 2.00e-02 2.50e+03 ... (remaining 5122 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6823 2.76 - 3.30: 44937 3.30 - 3.83: 102271 3.83 - 4.37: 124222 4.37 - 4.90: 174355 Nonbonded interactions: 452608 Sorted by model distance: nonbonded pdb=" O SER Q 66 " pdb=" NH1 ARG Q 70 " model vdw 2.228 2.520 nonbonded pdb=" O6 G A 78 " pdb=" O4 U A 86 " model vdw 2.237 2.432 nonbonded pdb=" N3 A A 352 " pdb=" O2' U A 364 " model vdw 2.241 2.520 nonbonded pdb=" O ILE U 85 " pdb=" OG1 THR U 89 " model vdw 2.249 2.440 nonbonded pdb=" O VAL U 103 " pdb=" NZ LYS U 139 " model vdw 2.251 2.520 ... (remaining 452603 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 10.430 Check model and map are aligned: 0.810 Set scattering table: 0.530 Process input model: 179.720 Find NCS groups from input model: 1.070 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 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 0.043 55042 Z= 0.477 Angle : 1.093 9.592 81211 Z= 0.691 Chirality : 0.100 0.752 10151 Planarity : 0.004 0.018 5125 Dihedral : 23.039 178.616 30655 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.40 % Favored : 93.37 % Rotamer: Outliers : 0.27 % Allowed : 4.19 % Favored : 95.54 % Cbeta Deviations : 0.12 % 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: -0.50 (0.16), residues: 2595 helix: 0.65 (0.16), residues: 1041 sheet: 0.16 (0.26), residues: 420 loop : -1.45 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 138 HIS 0.007 0.002 HIS P 13 PHE 0.015 0.002 PHE D 79 TYR 0.016 0.002 TYR L 117 ARG 0.010 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 397 time to evaluate : 3.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7985 (tp-100) REVERT: C 139 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7404 (tp-100) REVERT: D 134 ASP cc_start: 0.8509 (p0) cc_final: 0.8265 (p0) REVERT: E 19 MET cc_start: 0.8255 (mmm) cc_final: 0.7888 (mmt) REVERT: E 72 GLN cc_start: 0.8535 (pm20) cc_final: 0.8099 (pm20) REVERT: F 92 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8505 (ttmm) REVERT: G 12 LEU cc_start: 0.8967 (mt) cc_final: 0.8744 (mt) REVERT: I 60 ASP cc_start: 0.7205 (m-30) cc_final: 0.6196 (p0) REVERT: K 54 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7946 (mtt180) REVERT: K 108 ILE cc_start: 0.9245 (mt) cc_final: 0.8902 (mt) REVERT: M 31 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8451 (ttpp) REVERT: M 35 GLU cc_start: 0.7939 (pt0) cc_final: 0.7577 (pt0) REVERT: O 59 MET cc_start: 0.9054 (mtt) cc_final: 0.8738 (mtt) REVERT: P 50 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8429 (ttmm) REVERT: S 18 LYS cc_start: 0.6963 (mttt) cc_final: 0.6737 (mttt) REVERT: T 37 SER cc_start: 0.8653 (t) cc_final: 0.8363 (t) REVERT: V 10 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7790 (ttm-80) outliers start: 6 outliers final: 1 residues processed: 401 average time/residue: 0.6939 time to fit residues: 453.1395 Evaluate side-chains 342 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 249 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 6.9990 chunk 297 optimal weight: 0.9980 chunk 165 optimal weight: 0.0870 chunk 101 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 356 optimal weight: 1.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 136 GLN C 162 GLN F 27 GLN G 84 ASN G 96 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN K 13 GLN S 47 HIS ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55042 Z= 0.194 Angle : 0.548 8.387 81211 Z= 0.286 Chirality : 0.035 0.336 10151 Planarity : 0.004 0.045 5125 Dihedral : 23.563 179.916 25172 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.68 % Rotamer: Outliers : 0.86 % Allowed : 9.74 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2595 helix: 1.23 (0.16), residues: 1071 sheet: 0.08 (0.26), residues: 446 loop : -1.18 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.005 0.001 HIS L 77 PHE 0.017 0.001 PHE G 62 TYR 0.013 0.001 TYR I 4 ARG 0.005 0.000 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 345 time to evaluate : 3.617 Fit side-chains revert: symmetry clash REVERT: B 37 ASN cc_start: 0.8468 (p0) cc_final: 0.8056 (p0) REVERT: B 113 HIS cc_start: 0.7223 (m170) cc_final: 0.6957 (m170) REVERT: B 212 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7875 (tp-100) REVERT: C 17 ASP cc_start: 0.7596 (t0) cc_final: 0.7097 (t0) REVERT: C 139 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7350 (tp-100) REVERT: E 41 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8775 (p) REVERT: E 72 GLN cc_start: 0.8538 (pm20) cc_final: 0.8126 (pm20) REVERT: F 1 MET cc_start: 0.6953 (tpt) cc_final: 0.6683 (tpp) REVERT: I 60 ASP cc_start: 0.7276 (m-30) cc_final: 0.6208 (p0) REVERT: K 108 ILE cc_start: 0.9206 (mt) cc_final: 0.8851 (mt) REVERT: K 111 ASP cc_start: 0.8513 (t70) cc_final: 0.8231 (t70) REVERT: M 23 TYR cc_start: 0.8534 (t80) cc_final: 0.8295 (t80) REVERT: M 35 GLU cc_start: 0.7849 (pt0) cc_final: 0.7534 (pt0) REVERT: O 7 GLU cc_start: 0.7889 (mp0) cc_final: 0.7481 (mp0) REVERT: O 59 MET cc_start: 0.9122 (mtt) cc_final: 0.8865 (mtt) REVERT: P 50 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8384 (ttmm) REVERT: R 41 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8514 (mtpp) REVERT: S 44 MET cc_start: 0.8398 (mtp) cc_final: 0.7957 (mtm) REVERT: T 85 MET cc_start: 0.8326 (mtp) cc_final: 0.7921 (mtm) outliers start: 19 outliers final: 14 residues processed: 354 average time/residue: 0.6385 time to fit residues: 374.1683 Evaluate side-chains 346 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 331 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 249 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 297 optimal weight: 0.7980 chunk 243 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 357 optimal weight: 5.9990 chunk 386 optimal weight: 8.9990 chunk 318 optimal weight: 5.9990 chunk 354 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 286 optimal weight: 0.9980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 136 GLN F 27 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 55042 Z= 0.274 Angle : 0.573 8.612 81211 Z= 0.298 Chirality : 0.037 0.379 10151 Planarity : 0.004 0.048 5125 Dihedral : 23.486 179.074 25172 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.09 % Favored : 93.76 % Rotamer: Outliers : 1.85 % Allowed : 12.08 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2595 helix: 1.17 (0.16), residues: 1076 sheet: 0.03 (0.26), residues: 449 loop : -1.19 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 24 HIS 0.006 0.001 HIS U 43 PHE 0.015 0.002 PHE H 31 TYR 0.016 0.002 TYR P 32 ARG 0.005 0.000 ARG V 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 337 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 ASN cc_start: 0.8490 (p0) cc_final: 0.8045 (p0) REVERT: B 113 HIS cc_start: 0.7141 (m170) cc_final: 0.6881 (m170) REVERT: B 212 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7765 (tp-100) REVERT: C 139 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7341 (tp-100) REVERT: D 134 ASP cc_start: 0.8552 (p0) cc_final: 0.8241 (p0) REVERT: E 19 MET cc_start: 0.8442 (mmm) cc_final: 0.8022 (mmt) REVERT: E 72 GLN cc_start: 0.8539 (pm20) cc_final: 0.8121 (pm20) REVERT: I 60 ASP cc_start: 0.7367 (m-30) cc_final: 0.6234 (p0) REVERT: K 108 ILE cc_start: 0.9205 (mt) cc_final: 0.8848 (mt) REVERT: K 111 ASP cc_start: 0.8662 (t70) cc_final: 0.8381 (t70) REVERT: M 69 GLU cc_start: 0.7973 (pm20) cc_final: 0.7736 (pm20) REVERT: O 7 GLU cc_start: 0.7979 (mp0) cc_final: 0.7512 (mp0) REVERT: P 50 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8407 (ttmm) REVERT: R 41 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8600 (mtpp) REVERT: T 46 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7293 (mm-30) REVERT: T 85 MET cc_start: 0.8459 (mtp) cc_final: 0.8132 (mtm) outliers start: 41 outliers final: 31 residues processed: 360 average time/residue: 0.6503 time to fit residues: 386.9809 Evaluate side-chains 359 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 328 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 249 GLU Chi-restraints excluded: chain U residue 264 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 358 optimal weight: 9.9990 chunk 379 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN F 27 GLN G 84 ASN J 13 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 55042 Z= 0.424 Angle : 0.668 9.013 81211 Z= 0.343 Chirality : 0.042 0.350 10151 Planarity : 0.005 0.052 5125 Dihedral : 23.513 178.312 25172 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.55 % Favored : 93.29 % Rotamer: Outliers : 2.66 % Allowed : 13.44 % Favored : 83.90 % 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: -0.26 (0.17), residues: 2595 helix: 0.92 (0.16), residues: 1067 sheet: -0.04 (0.26), residues: 436 loop : -1.30 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 24 HIS 0.008 0.002 HIS N 49 PHE 0.015 0.002 PHE U 195 TYR 0.019 0.002 TYR P 32 ARG 0.006 0.001 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 336 time to evaluate : 3.853 Fit side-chains REVERT: B 37 ASN cc_start: 0.8469 (p0) cc_final: 0.8044 (p0) REVERT: B 135 GLN cc_start: 0.8145 (mt0) cc_final: 0.7799 (mt0) REVERT: B 212 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7828 (tp-100) REVERT: C 139 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7321 (tp-100) REVERT: E 72 GLN cc_start: 0.8554 (pm20) cc_final: 0.8134 (pm20) REVERT: F 1 MET cc_start: 0.7216 (tpt) cc_final: 0.6979 (tpp) REVERT: I 60 ASP cc_start: 0.7410 (m-30) cc_final: 0.6245 (p0) REVERT: K 108 ILE cc_start: 0.9241 (mt) cc_final: 0.8927 (mt) REVERT: K 111 ASP cc_start: 0.8729 (t70) cc_final: 0.8517 (t70) REVERT: M 9 ILE cc_start: 0.8305 (mm) cc_final: 0.8093 (mm) REVERT: M 69 GLU cc_start: 0.7946 (pm20) cc_final: 0.7509 (pm20) REVERT: N 17 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8673 (mtpt) REVERT: O 7 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7716 (mp0) REVERT: P 50 LYS cc_start: 0.8761 (ttmt) cc_final: 0.8433 (ttmm) REVERT: R 41 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8530 (mtpp) REVERT: T 85 MET cc_start: 0.8499 (mtp) cc_final: 0.8145 (mtm) outliers start: 59 outliers final: 46 residues processed: 370 average time/residue: 0.6388 time to fit residues: 392.3786 Evaluate side-chains 377 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 331 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 212 ASP Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain U residue 264 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 324 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS C 98 ASN F 27 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55042 Z= 0.181 Angle : 0.536 10.013 81211 Z= 0.280 Chirality : 0.035 0.300 10151 Planarity : 0.004 0.049 5125 Dihedral : 23.441 179.191 25169 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 2.03 % Allowed : 15.15 % Favored : 82.82 % 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: 0.08 (0.17), residues: 2595 helix: 1.23 (0.16), residues: 1077 sheet: 0.05 (0.26), residues: 437 loop : -1.14 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 138 HIS 0.005 0.001 HIS B 113 PHE 0.011 0.001 PHE G 62 TYR 0.013 0.001 TYR C 48 ARG 0.006 0.000 ARG V 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 339 time to evaluate : 4.133 Fit side-chains revert: symmetry clash REVERT: B 33 TYR cc_start: 0.8709 (t80) cc_final: 0.8404 (t80) REVERT: B 212 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7745 (tp-100) REVERT: C 139 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7315 (tp-100) REVERT: C 193 TYR cc_start: 0.8390 (p90) cc_final: 0.8159 (p90) REVERT: E 41 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8750 (p) REVERT: E 72 GLN cc_start: 0.8481 (pm20) cc_final: 0.8081 (pm20) REVERT: F 1 MET cc_start: 0.7072 (tpt) cc_final: 0.6787 (mmm) REVERT: F 63 TYR cc_start: 0.8527 (m-80) cc_final: 0.8243 (m-10) REVERT: G 86 GLN cc_start: 0.8651 (mp10) cc_final: 0.8398 (mm-40) REVERT: I 60 ASP cc_start: 0.7355 (m-30) cc_final: 0.6196 (p0) REVERT: J 86 MET cc_start: 0.7792 (mpp) cc_final: 0.7565 (mpp) REVERT: K 108 ILE cc_start: 0.9249 (mt) cc_final: 0.8938 (mt) REVERT: M 34 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7774 (tt) REVERT: P 50 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8327 (ttmm) REVERT: R 41 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8494 (mtpp) REVERT: S 43 GLU cc_start: 0.8366 (mp0) cc_final: 0.8150 (mp0) REVERT: T 46 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7529 (mm-30) REVERT: T 85 MET cc_start: 0.8465 (mtp) cc_final: 0.8158 (mtm) REVERT: T 92 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8003 (mm) REVERT: U 183 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6297 (mp0) outliers start: 45 outliers final: 32 residues processed: 366 average time/residue: 0.6530 time to fit residues: 396.4314 Evaluate side-chains 367 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 331 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 183 GLU Chi-restraints excluded: chain U residue 264 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 10.0000 chunk 342 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 380 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN F 27 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 234 GLN U 246 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 55042 Z= 0.471 Angle : 0.698 9.958 81211 Z= 0.354 Chirality : 0.043 0.307 10151 Planarity : 0.006 0.054 5125 Dihedral : 23.495 178.198 25169 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.86 % Favored : 93.03 % Rotamer: Outliers : 3.52 % Allowed : 14.92 % Favored : 81.56 % 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: -0.29 (0.17), residues: 2595 helix: 0.89 (0.16), residues: 1070 sheet: -0.17 (0.26), residues: 436 loop : -1.26 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 24 HIS 0.010 0.002 HIS N 49 PHE 0.015 0.002 PHE C 203 TYR 0.021 0.002 TYR L 117 ARG 0.006 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 321 time to evaluate : 4.032 Fit side-chains revert: symmetry clash REVERT: B 33 TYR cc_start: 0.8705 (t80) cc_final: 0.8425 (t80) REVERT: B 135 GLN cc_start: 0.8163 (mt0) cc_final: 0.7822 (mt0) REVERT: B 212 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7751 (tp-100) REVERT: C 139 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7322 (tp-100) REVERT: E 72 GLN cc_start: 0.8490 (pm20) cc_final: 0.8094 (pm20) REVERT: I 60 ASP cc_start: 0.7571 (m-30) cc_final: 0.6252 (p0) REVERT: K 108 ILE cc_start: 0.9257 (mt) cc_final: 0.8939 (mt) REVERT: P 50 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8437 (ttmm) REVERT: R 41 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8514 (mtpp) REVERT: S 43 GLU cc_start: 0.8297 (mp0) cc_final: 0.8094 (mp0) REVERT: T 51 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7842 (mm-30) REVERT: T 85 MET cc_start: 0.8478 (mtp) cc_final: 0.8137 (mtm) REVERT: U 46 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.7028 (t) outliers start: 78 outliers final: 61 residues processed: 372 average time/residue: 0.6375 time to fit residues: 393.9816 Evaluate side-chains 383 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 321 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 15 MET Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 128 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 212 ASP Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain U residue 264 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 277 optimal weight: 0.0470 chunk 215 optimal weight: 0.9990 chunk 320 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 378 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 136 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 55042 Z= 0.132 Angle : 0.526 10.614 81211 Z= 0.274 Chirality : 0.035 0.233 10151 Planarity : 0.004 0.047 5125 Dihedral : 23.424 178.826 25169 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.05 % Favored : 94.80 % Rotamer: Outliers : 2.21 % Allowed : 16.41 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2595 helix: 1.33 (0.16), residues: 1076 sheet: 0.08 (0.26), residues: 432 loop : -1.11 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 138 HIS 0.003 0.001 HIS U 144 PHE 0.013 0.001 PHE G 62 TYR 0.013 0.001 TYR G 85 ARG 0.006 0.000 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 345 time to evaluate : 4.746 Fit side-chains revert: symmetry clash REVERT: B 33 TYR cc_start: 0.8666 (t80) cc_final: 0.8379 (t80) REVERT: B 212 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7713 (tp-100) REVERT: C 17 ASP cc_start: 0.7451 (t0) cc_final: 0.7208 (t0) REVERT: C 139 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7301 (tp-100) REVERT: E 41 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8731 (p) REVERT: E 72 GLN cc_start: 0.8454 (pm20) cc_final: 0.8076 (pm20) REVERT: F 63 TYR cc_start: 0.8498 (m-80) cc_final: 0.8214 (m-10) REVERT: G 86 GLN cc_start: 0.8644 (mp10) cc_final: 0.8423 (mm-40) REVERT: I 60 ASP cc_start: 0.7323 (m-30) cc_final: 0.6169 (p0) REVERT: J 86 MET cc_start: 0.7803 (mpp) cc_final: 0.7552 (mpp) REVERT: K 108 ILE cc_start: 0.9246 (mt) cc_final: 0.8975 (mt) REVERT: M 34 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7588 (tt) REVERT: M 65 LYS cc_start: 0.7364 (tppp) cc_final: 0.7137 (tppp) REVERT: P 50 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8354 (ttmm) REVERT: R 41 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8465 (mtpp) REVERT: S 43 GLU cc_start: 0.8328 (mp0) cc_final: 0.8090 (mp0) REVERT: T 46 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7277 (mm-30) REVERT: T 51 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7896 (mm-30) REVERT: T 85 MET cc_start: 0.8404 (mtp) cc_final: 0.8091 (mtm) outliers start: 49 outliers final: 34 residues processed: 375 average time/residue: 0.6256 time to fit residues: 387.7265 Evaluate side-chains 370 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 334 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 264 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 226 optimal weight: 0.2980 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 240 optimal weight: 0.4980 chunk 258 optimal weight: 0.0980 chunk 187 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 297 optimal weight: 0.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN D 45 GLN F 27 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 55042 Z= 0.114 Angle : 0.486 8.360 81211 Z= 0.252 Chirality : 0.032 0.212 10151 Planarity : 0.004 0.048 5125 Dihedral : 23.349 178.338 25169 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.84 % Rotamer: Outliers : 1.76 % Allowed : 16.95 % Favored : 81.29 % 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: 0.45 (0.17), residues: 2595 helix: 1.58 (0.16), residues: 1076 sheet: 0.30 (0.27), residues: 418 loop : -0.99 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 138 HIS 0.003 0.001 HIS U 144 PHE 0.013 0.001 PHE G 62 TYR 0.019 0.001 TYR C 193 ARG 0.007 0.000 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 359 time to evaluate : 3.584 Fit side-chains revert: symmetry clash REVERT: B 33 TYR cc_start: 0.8645 (t80) cc_final: 0.8391 (t80) REVERT: B 212 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7548 (tp-100) REVERT: C 17 ASP cc_start: 0.7279 (t0) cc_final: 0.7036 (t0) REVERT: C 139 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7257 (tp-100) REVERT: D 161 ASN cc_start: 0.8558 (m-40) cc_final: 0.8295 (m-40) REVERT: E 72 GLN cc_start: 0.8458 (pm20) cc_final: 0.8124 (pm20) REVERT: F 63 TYR cc_start: 0.8408 (m-80) cc_final: 0.8071 (m-10) REVERT: I 60 ASP cc_start: 0.7531 (m-30) cc_final: 0.6250 (p0) REVERT: J 86 MET cc_start: 0.7831 (mpp) cc_final: 0.7580 (mpp) REVERT: J 90 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6122 (mt) REVERT: K 77 MET cc_start: 0.8100 (mtt) cc_final: 0.7814 (mtt) REVERT: K 108 ILE cc_start: 0.9276 (mt) cc_final: 0.8998 (mt) REVERT: M 34 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7687 (tt) REVERT: M 65 LYS cc_start: 0.7169 (tppp) cc_final: 0.6826 (tppp) REVERT: P 50 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8334 (ttmm) REVERT: R 36 ASN cc_start: 0.8514 (t0) cc_final: 0.8231 (t0) REVERT: R 41 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8438 (mtpp) REVERT: T 45 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7850 (tm-30) REVERT: T 46 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6798 (mm-30) REVERT: T 48 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7506 (mppt) REVERT: T 85 MET cc_start: 0.8397 (mtp) cc_final: 0.8077 (mtm) outliers start: 39 outliers final: 22 residues processed: 382 average time/residue: 0.6631 time to fit residues: 415.9252 Evaluate side-chains 363 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 338 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 48 LYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain U residue 264 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 331 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 333 optimal weight: 4.9990 chunk 351 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 HIS ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 55042 Z= 0.379 Angle : 0.631 9.101 81211 Z= 0.320 Chirality : 0.038 0.267 10151 Planarity : 0.005 0.051 5125 Dihedral : 23.364 178.214 25169 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 1.98 % Allowed : 17.31 % Favored : 80.70 % 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: 0.13 (0.17), residues: 2595 helix: 1.30 (0.16), residues: 1066 sheet: -0.01 (0.26), residues: 443 loop : -1.08 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 24 HIS 0.005 0.001 HIS J 56 PHE 0.024 0.002 PHE G 62 TYR 0.029 0.002 TYR G 154 ARG 0.007 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 322 time to evaluate : 3.648 Fit side-chains REVERT: B 33 TYR cc_start: 0.8685 (t80) cc_final: 0.8444 (t80) REVERT: B 212 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7672 (tp-100) REVERT: C 139 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7310 (tp-100) REVERT: E 72 GLN cc_start: 0.8511 (pm20) cc_final: 0.8076 (pm20) REVERT: F 63 TYR cc_start: 0.8540 (m-80) cc_final: 0.8198 (m-10) REVERT: I 60 ASP cc_start: 0.7581 (m-30) cc_final: 0.6263 (p0) REVERT: J 86 MET cc_start: 0.7732 (mpp) cc_final: 0.7495 (mpp) REVERT: J 90 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6441 (mt) REVERT: K 108 ILE cc_start: 0.9263 (mt) cc_final: 0.8940 (mt) REVERT: P 50 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8428 (ttmm) REVERT: R 41 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8468 (mtpp) REVERT: S 40 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7450 (mp) REVERT: S 44 MET cc_start: 0.8491 (mtp) cc_final: 0.8221 (mtt) REVERT: T 85 MET cc_start: 0.8557 (mtp) cc_final: 0.8248 (mtm) REVERT: T 90 GLN cc_start: 0.7956 (mt0) cc_final: 0.7734 (tm-30) outliers start: 44 outliers final: 28 residues processed: 350 average time/residue: 0.6656 time to fit residues: 384.7872 Evaluate side-chains 350 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 320 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain U residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 8.9990 chunk 373 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 259 optimal weight: 0.2980 chunk 391 optimal weight: 0.9980 chunk 360 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 ASN S 47 HIS ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55042 Z= 0.171 Angle : 0.530 8.777 81211 Z= 0.274 Chirality : 0.034 0.236 10151 Planarity : 0.004 0.050 5125 Dihedral : 23.325 177.360 25169 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.53 % Rotamer: Outliers : 1.35 % Allowed : 18.44 % Favored : 80.21 % 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: 0.29 (0.17), residues: 2595 helix: 1.43 (0.16), residues: 1076 sheet: 0.15 (0.26), residues: 434 loop : -1.05 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.013 0.001 HIS U 43 PHE 0.010 0.001 PHE D 79 TYR 0.025 0.001 TYR C 193 ARG 0.008 0.000 ARG F 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 329 time to evaluate : 3.714 Fit side-chains revert: symmetry clash REVERT: B 33 TYR cc_start: 0.8667 (t80) cc_final: 0.8432 (t80) REVERT: B 212 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7725 (tp-100) REVERT: C 139 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7304 (tp-100) REVERT: E 72 GLN cc_start: 0.8464 (pm20) cc_final: 0.8044 (pm20) REVERT: F 63 TYR cc_start: 0.8503 (m-80) cc_final: 0.8145 (m-10) REVERT: G 16 LEU cc_start: 0.8714 (mp) cc_final: 0.8448 (mp) REVERT: I 60 ASP cc_start: 0.7513 (m-30) cc_final: 0.6257 (p0) REVERT: J 86 MET cc_start: 0.7884 (mpp) cc_final: 0.7623 (mpp) REVERT: J 90 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6371 (mt) REVERT: K 108 ILE cc_start: 0.9253 (mt) cc_final: 0.8986 (mt) REVERT: M 34 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7724 (tt) REVERT: P 50 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8346 (ttmm) REVERT: R 41 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8470 (mtpp) REVERT: S 44 MET cc_start: 0.8481 (mtp) cc_final: 0.8151 (mtt) REVERT: T 46 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7244 (mm-30) REVERT: T 50 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7044 (pm20) REVERT: T 85 MET cc_start: 0.8495 (mtp) cc_final: 0.8188 (mtm) outliers start: 30 outliers final: 23 residues processed: 344 average time/residue: 0.6491 time to fit residues: 367.0060 Evaluate side-chains 350 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 325 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain U residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 7.9990 chunk 332 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 HIS ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.046248 restraints weight = 152558.693| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 1.29 r_work: 0.2463 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 55042 Z= 0.446 Angle : 0.688 12.431 81211 Z= 0.348 Chirality : 0.042 0.309 10151 Planarity : 0.005 0.056 5125 Dihedral : 23.410 178.134 25169 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.01 % Favored : 92.87 % Rotamer: Outliers : 1.94 % Allowed : 17.90 % Favored : 80.16 % 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: -0.13 (0.17), residues: 2595 helix: 1.07 (0.16), residues: 1066 sheet: -0.16 (0.26), residues: 443 loop : -1.20 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 24 HIS 0.007 0.002 HIS N 49 PHE 0.015 0.002 PHE U 195 TYR 0.030 0.002 TYR G 154 ARG 0.008 0.001 ARG D 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9444.34 seconds wall clock time: 173 minutes 55.70 seconds (10435.70 seconds total)