Starting phenix.real_space_refine on Sun Nov 19 14:26:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/11_2023/6ppk_20441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/11_2023/6ppk_20441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/11_2023/6ppk_20441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/11_2023/6ppk_20441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/11_2023/6ppk_20441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/11_2023/6ppk_20441_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 2773 5.49 5 S 65 5.16 5 C 39667 2.51 5 N 14963 2.21 5 O 22983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "P ARG 42": "NH1" <-> "NH2" Residue "P PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 115": "OE1" <-> "OE2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "W GLU 243": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 80451 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 57112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2658, 57112 Classifications: {'RNA': 2658} Modifications used: {'rna2p_pur': 253, 'rna2p_pyr': 132, 'rna3p_pur': 1302, 'rna3p_pyr': 971} Link IDs: {'rna2p': 385, 'rna3p': 2272} Chain breaks: 14 Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 53, 'rna3p_pyr': 44} Link IDs: {'rna2p': 15, 'rna3p': 96} Chain: "C" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2010 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 16, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1511 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain breaks: 3 Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 829 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1119 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 904 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain breaks: 1 Chain: "N" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 947 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "O" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 3 Chain: "P" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 724 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "U" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 691 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 2 Chain: "V" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 604 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain breaks: 1 Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 418 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1990 Unusual residues: {'GNP': 1} Classifications: {'peptide': 252, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 239, None: 1} Not linked: pdbres="GLN W 279 " pdbres="GNP W 301 " Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 30.57, per 1000 atoms: 0.38 Number of scatterers: 80451 At special positions: 0 Unit cell: (203, 210.25, 217.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 2773 15.00 O 22983 8.00 N 14963 7.00 C 39667 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 Atom "ATOM 58212 O4' U B 54 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.68 Conformation dependent library (CDL) restraints added in 3.2 seconds 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 27 sheets defined 23.7% alpha, 10.5% beta 645 base pairs and 1304 stacking pairs defined. Time for finding SS restraints: 39.52 Creating SS restraints... Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.785A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 4.300A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.703A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.591A pdb=" N GLY D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 67' Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'E' and resid 30 through 41 removed outlier: 3.609A pdb=" N MET E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 119 removed outlier: 3.625A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 4.268A pdb=" N GLY E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 183 through 189 removed outlier: 4.150A pdb=" N VAL E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 205 Processing helix chain 'F' and resid 12 through 15 No H-bonds generated for 'chain 'F' and resid 12 through 15' Processing helix chain 'F' and resid 95 through 106 removed outlier: 3.526A pdb=" N ILE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'G' and resid 61 through 81 Processing helix chain 'G' and resid 139 through 150 removed outlier: 3.737A pdb=" N ALA G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA G 146 " --> pdb=" O VAL G 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 90 through 96 Processing helix chain 'J' and resid 98 through 109 removed outlier: 3.860A pdb=" N ALA J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE J 106 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'L' and resid 95 through 98 No H-bonds generated for 'chain 'L' and resid 95 through 98' Processing helix chain 'L' and resid 130 through 136 removed outlier: 3.783A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 27 removed outlier: 3.624A pdb=" N ALA N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU N 17 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU N 20 " --> pdb=" O MET N 16 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 51 removed outlier: 4.832A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 63 removed outlier: 3.523A pdb=" N GLN N 61 " --> pdb=" O HIS N 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 91 removed outlier: 3.623A pdb=" N LEU N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER N 85 " --> pdb=" O GLN N 81 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA N 88 " --> pdb=" O PHE N 84 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N THR N 89 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 20 Processing helix chain 'O' and resid 80 through 83 No H-bonds generated for 'chain 'O' and resid 80 through 83' Processing helix chain 'O' and resid 85 through 87 No H-bonds generated for 'chain 'O' and resid 85 through 87' Processing helix chain 'O' and resid 105 through 115 Processing helix chain 'P' and resid 6 through 15 removed outlier: 4.234A pdb=" N ASP P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU P 14 " --> pdb=" O ASP P 10 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN P 15 " --> pdb=" O ILE P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 6 through 15' Processing helix chain 'P' and resid 57 through 59 No H-bonds generated for 'chain 'P' and resid 57 through 59' Processing helix chain 'P' and resid 101 through 104 Processing helix chain 'P' and resid 113 through 115 No H-bonds generated for 'chain 'P' and resid 113 through 115' Processing helix chain 'Q' and resid 9 through 21 removed outlier: 3.868A pdb=" N LYS Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 29 removed outlier: 4.048A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 26 through 29' Processing helix chain 'Q' and resid 32 through 35 No H-bonds generated for 'chain 'Q' and resid 32 through 35' Processing helix chain 'Q' and resid 39 through 72 removed outlier: 3.849A pdb=" N ASN Q 44 " --> pdb=" O MET Q 40 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE Q 62 " --> pdb=" O ARG Q 58 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA Q 68 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 85 removed outlier: 3.918A pdb=" N LEU Q 85 " --> pdb=" O HIS Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 98 Processing helix chain 'Q' and resid 107 through 114 removed outlier: 4.196A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 23 removed outlier: 3.603A pdb=" N VAL S 20 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP S 22 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 35 removed outlier: 4.104A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 removed outlier: 3.768A pdb=" N VAL S 50 " --> pdb=" O ILE S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 15 through 21 Processing helix chain 'T' and resid 36 through 46 removed outlier: 3.542A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 16 No H-bonds generated for 'chain 'U' and resid 14 through 16' Processing helix chain 'U' and resid 65 through 67 No H-bonds generated for 'chain 'U' and resid 65 through 67' Processing helix chain 'Z' and resid 17 through 26 removed outlier: 3.532A pdb=" N VAL Z 21 " --> pdb=" O GLU Z 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR Z 22 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 49 removed outlier: 4.258A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Z 47 " --> pdb=" O ILE Z 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 20 No H-bonds generated for 'chain 'b' and resid 18 through 20' Processing helix chain 'Y' and resid 11 through 34 removed outlier: 4.978A pdb=" N GLN Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS Y 17 " --> pdb=" O GLU Y 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS Y 19 " --> pdb=" O GLU Y 15 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER Y 20 " --> pdb=" O GLN Y 16 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 64 removed outlier: 3.994A pdb=" N ARG Y 47 " --> pdb=" O ILE Y 43 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 15 Processing helix chain 'd' and resid 25 through 37 removed outlier: 3.597A pdb=" N LEU d 31 " --> pdb=" O GLY d 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 20 removed outlier: 3.509A pdb=" N GLU W 16 " --> pdb=" O LYS W 12 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU W 19 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS W 20 " --> pdb=" O GLU W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 39 No H-bonds generated for 'chain 'W' and resid 37 through 39' Processing helix chain 'W' and resid 44 through 47 No H-bonds generated for 'chain 'W' and resid 44 through 47' Processing helix chain 'W' and resid 66 through 78 Processing helix chain 'W' and resid 99 through 102 No H-bonds generated for 'chain 'W' and resid 99 through 102' Processing helix chain 'W' and resid 105 through 107 No H-bonds generated for 'chain 'W' and resid 105 through 107' Processing helix chain 'W' and resid 190 through 192 No H-bonds generated for 'chain 'W' and resid 190 through 192' Processing helix chain 'W' and resid 203 through 215 removed outlier: 4.092A pdb=" N LEU W 210 " --> pdb=" O ALA W 206 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG W 211 " --> pdb=" O VAL W 207 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE W 212 " --> pdb=" O PHE W 208 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 224 removed outlier: 3.926A pdb=" N LEU W 221 " --> pdb=" O PRO W 218 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS W 222 " --> pdb=" O GLU W 219 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU W 223 " --> pdb=" O ARG W 220 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG W 224 " --> pdb=" O LEU W 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 218 through 224' Processing helix chain 'W' and resid 236 through 245 removed outlier: 3.710A pdb=" N LYS W 244 " --> pdb=" O ALA W 240 " (cutoff:3.500A) Processing helix chain 'W' and resid 256 through 267 removed outlier: 3.717A pdb=" N ILE W 263 " --> pdb=" O THR W 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP W 266 " --> pdb=" O VAL W 262 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= B, first strand: chain 'C' and resid 115 through 117 removed outlier: 4.687A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 102 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'C' and resid 172 through 175 removed outlier: 3.564A pdb=" N ARG C 182 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 4 through 8 removed outlier: 7.038A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 12 through 15 Processing sheet with id= G, first strand: chain 'D' and resid 175 through 180 removed outlier: 4.515A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 123 through 125 removed outlier: 6.134A pdb=" N LEU E 192 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 174 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 89 through 91 removed outlier: 4.156A pdb=" N LEU F 91 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 162 through 165 removed outlier: 4.306A pdb=" N VAL G 91 " --> pdb=" O GLY G 162 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 103 through 105 removed outlier: 3.512A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 18 through 20 removed outlier: 6.126A pdb=" N ILE J 56 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN J 124 " --> pdb=" O VAL J 55 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 7 through 9 removed outlier: 7.235A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 75 through 77 removed outlier: 3.955A pdb=" N LYS L 110 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 77 " --> pdb=" O LYS L 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.485A pdb=" N GLY N 105 " --> pdb=" O MET N 114 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE N 116 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS N 103 " --> pdb=" O ILE N 116 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLU N 118 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE N 101 " --> pdb=" O GLU N 118 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 44 through 49 removed outlier: 3.667A pdb=" N THR P 28 " --> pdb=" O ARG P 91 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG P 30 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL P 89 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N HIS P 32 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE P 87 " --> pdb=" O HIS P 32 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 64 through 68 Processing sheet with id= R, first strand: chain 'R' and resid 3 through 5 Processing sheet with id= S, first strand: chain 'R' and resid 19 through 22 removed outlier: 4.108A pdb=" N GLY R 66 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'R' and resid 71 through 76 removed outlier: 3.687A pdb=" N ILE R 71 " --> pdb=" O HIS R 88 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 3 through 6 removed outlier: 3.721A pdb=" N GLN S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER S 108 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'S' and resid 84 through 86 removed outlier: 3.681A pdb=" N ARG S 86 " --> pdb=" O SER S 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER S 94 " --> pdb=" O ARG S 86 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'T' and resid 25 through 29 removed outlier: 3.581A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'U' and resid 23 through 27 removed outlier: 6.671A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'V' and resid 74 through 80 Processing sheet with id= Z, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.768A pdb=" N THR Z 7 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'W' and resid 123 through 125 removed outlier: 7.307A pdb=" N ILE W 26 " --> pdb=" O LEU W 124 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN W 58 " --> pdb=" O VAL W 31 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1520 hydrogen bonds 2308 hydrogen bond angles 0 basepair planarities 645 basepair parallelities 1304 stacking parallelities Total time for adding SS restraints: 101.87 Time building geometry restraints manager: 43.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8834 1.32 - 1.44: 38759 1.44 - 1.56: 34598 1.56 - 1.69: 5530 1.69 - 1.81: 124 Bond restraints: 87845 Sorted by residual: bond pdb=" C GLN d 6 " pdb=" N PRO d 7 " ideal model delta sigma weight residual 1.335 1.285 0.050 8.70e-03 1.32e+04 3.25e+01 bond pdb=" O2B GNP W 301 " pdb=" PB GNP W 301 " ideal model delta sigma weight residual 1.505 1.610 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C4 GNP W 301 " pdb=" C5 GNP W 301 " ideal model delta sigma weight residual 1.382 1.470 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O2G GNP W 301 " pdb=" PG GNP W 301 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O3G GNP W 301 " pdb=" PG GNP W 301 " ideal model delta sigma weight residual 1.532 1.610 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 87840 not shown) Histogram of bond angle deviations from ideal: 92.19 - 101.26: 874 101.26 - 110.34: 45707 110.34 - 119.41: 45907 119.41 - 128.48: 36100 128.48 - 137.56: 3754 Bond angle restraints: 132342 Sorted by residual: angle pdb=" C ILE K 2 " pdb=" CA ILE K 2 " pdb=" CB ILE K 2 " ideal model delta sigma weight residual 111.49 137.56 -26.07 1.38e+00 5.25e-01 3.57e+02 angle pdb=" C ARG V 82 " pdb=" CA ARG V 82 " pdb=" CB ARG V 82 " ideal model delta sigma weight residual 111.26 134.21 -22.95 1.66e+00 3.63e-01 1.91e+02 angle pdb=" N ARG V 82 " pdb=" CA ARG V 82 " pdb=" C ARG V 82 " ideal model delta sigma weight residual 112.12 95.34 16.78 1.34e+00 5.57e-01 1.57e+02 angle pdb=" N ILE K 2 " pdb=" CA ILE K 2 " pdb=" C ILE K 2 " ideal model delta sigma weight residual 109.45 92.19 17.26 1.39e+00 5.18e-01 1.54e+02 angle pdb=" N LYS U 84 " pdb=" CA LYS U 84 " pdb=" C LYS U 84 " ideal model delta sigma weight residual 112.93 127.69 -14.76 1.33e+00 5.65e-01 1.23e+02 ... (remaining 132337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 42741 35.96 - 71.93: 3250 71.93 - 107.89: 305 107.89 - 143.86: 31 143.86 - 179.82: 51 Dihedral angle restraints: 46378 sinusoidal: 38782 harmonic: 7596 Sorted by residual: dihedral pdb=" O4' C A1281 " pdb=" C1' C A1281 " pdb=" N1 C A1281 " pdb=" C2 C A1281 " ideal model delta sinusoidal sigma weight residual -160.00 19.45 -179.45 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1515 " pdb=" C1' C A1515 " pdb=" N1 C A1515 " pdb=" C2 C A1515 " ideal model delta sinusoidal sigma weight residual 200.00 46.15 153.85 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' C A 482 " pdb=" C1' C A 482 " pdb=" N1 C A 482 " pdb=" C2 C A 482 " ideal model delta sinusoidal sigma weight residual 200.00 47.90 152.10 1 1.50e+01 4.44e-03 8.04e+01 ... (remaining 46375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 16497 0.123 - 0.247: 521 0.247 - 0.370: 36 0.370 - 0.493: 7 0.493 - 0.617: 5 Chirality restraints: 17066 Sorted by residual: chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 1.82 0.62 2.00e-01 2.50e+01 9.51e+00 chirality pdb=" CA SER D 103 " pdb=" N SER D 103 " pdb=" C SER D 103 " pdb=" CB SER D 103 " both_signs ideal model delta sigma weight residual False 2.51 3.09 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CA LEU P 29 " pdb=" N LEU P 29 " pdb=" C LEU P 29 " pdb=" CB LEU P 29 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 17063 not shown) Planarity restraints: 6406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 50 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO R 51 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 51 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 51 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 4 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO J 5 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO J 5 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 5 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 248 " 0.049 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO C 249 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 249 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 249 " 0.040 5.00e-02 4.00e+02 ... (remaining 6403 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 36 1.90 - 2.65: 5166 2.65 - 3.40: 110790 3.40 - 4.15: 268701 4.15 - 4.90: 353518 Nonbonded interactions: 738211 Sorted by model distance: nonbonded pdb=" CD LYS F 33 " pdb=" NH2 ARG F 92 " model vdw 1.150 3.520 nonbonded pdb=" O4' A B 55 " pdb=" OE1 GLN F 27 " model vdw 1.152 3.040 nonbonded pdb=" OD2 ASP D 54 " pdb=" NH1 ARG D 78 " model vdw 1.177 2.520 nonbonded pdb=" OD1 ASP U 72 " pdb=" NE2 GLN U 99 " model vdw 1.245 2.520 nonbonded pdb=" O2 C B 41 " pdb=" CD ARG F 92 " model vdw 1.329 3.440 ... (remaining 738206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 6.490 Check model and map are aligned: 0.900 Set scattering table: 0.570 Process input model: 264.490 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 277.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 0.134 87845 Z= 0.500 Angle : 1.080 26.069 132342 Z= 0.548 Chirality : 0.054 0.617 17066 Planarity : 0.006 0.079 6406 Dihedral : 20.237 179.820 41488 Min Nonbonded Distance : 1.150 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.81 % Favored : 87.54 % Rotamer: Outliers : 8.03 % Allowed : 13.19 % Favored : 78.78 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.28 (0.13), residues: 2608 helix: -3.33 (0.14), residues: 587 sheet: -2.46 (0.24), residues: 396 loop : -2.87 (0.13), residues: 1625 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 785 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 39 residues processed: 890 average time/residue: 0.8830 time to fit residues: 1306.0469 Evaluate side-chains 536 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 497 time to evaluate : 3.361 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.7769 time to fit residues: 55.9032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 451 optimal weight: 3.9990 chunk 405 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 419 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 312 optimal weight: 4.9990 chunk 485 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 197 ASN C 228 ASN C 264 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS D 152 ASN D 184 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS J 96 ASN J 124 ASN L 78 ASN N 61 GLN N 75 ASN N 81 GLN P 15 GLN P 32 HIS ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 44 ASN ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 60 HIS U 20 GLN U 67 ASN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 GLN Y 36 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 HIS W 78 GLN W 130 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 87845 Z= 0.297 Angle : 0.782 11.012 132342 Z= 0.388 Chirality : 0.041 0.311 17066 Planarity : 0.006 0.073 6406 Dihedral : 19.901 179.103 36132 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.16 % Favored : 90.76 % Rotamer: Outliers : 0.49 % Allowed : 6.46 % Favored : 93.05 % 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: -3.37 (0.15), residues: 2608 helix: -2.06 (0.18), residues: 628 sheet: -2.05 (0.24), residues: 435 loop : -2.44 (0.14), residues: 1545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 653 time to evaluate : 3.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 661 average time/residue: 0.8134 time to fit residues: 909.2275 Evaluate side-chains 464 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 460 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6462 time to fit residues: 8.2509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 270 optimal weight: 40.0000 chunk 150 optimal weight: 20.0000 chunk 404 optimal weight: 0.0870 chunk 330 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 chunk 525 optimal weight: 5.9990 chunk 433 optimal weight: 4.9990 chunk 482 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN C 264 ASN D 33 ASN D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 172 GLN G 66 HIS ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN K 4 GLN N 12 GLN O 103 HIS P 15 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** Q 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN S 61 ASN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 HIS b 40 HIS Y 39 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 216 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 87845 Z= 0.236 Angle : 0.691 10.293 132342 Z= 0.346 Chirality : 0.038 0.302 17066 Planarity : 0.005 0.076 6406 Dihedral : 19.666 179.456 36132 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.20 % Favored : 90.76 % Rotamer: Outliers : 0.45 % Allowed : 7.13 % Favored : 92.42 % 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: -2.72 (0.15), residues: 2608 helix: -1.35 (0.19), residues: 646 sheet: -1.67 (0.24), residues: 433 loop : -2.11 (0.15), residues: 1529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 606 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 614 average time/residue: 0.8314 time to fit residues: 873.6330 Evaluate side-chains 455 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 454 time to evaluate : 3.354 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6140 time to fit residues: 4.4651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 480 optimal weight: 9.9990 chunk 365 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 326 optimal weight: 7.9990 chunk 488 optimal weight: 20.0000 chunk 517 optimal weight: 40.0000 chunk 255 optimal weight: 20.0000 chunk 462 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS J 96 ASN J 124 ASN N 12 GLN N 75 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN S 60 HIS S 68 ASN U 58 ASN Z 37 HIS ** Z 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 4 ASN Y 39 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 87845 Z= 0.369 Angle : 0.800 11.987 132342 Z= 0.397 Chirality : 0.042 0.403 17066 Planarity : 0.006 0.072 6406 Dihedral : 19.982 178.961 36132 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 29.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.51 % Favored : 89.46 % Rotamer: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.15), residues: 2608 helix: -1.28 (0.19), residues: 641 sheet: -1.64 (0.25), residues: 406 loop : -2.07 (0.15), residues: 1561 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 541 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 543 average time/residue: 0.7838 time to fit residues: 726.5906 Evaluate side-chains 411 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 430 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 213 optimal weight: 30.0000 chunk 441 optimal weight: 10.0000 chunk 357 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 464 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 66 HIS J 96 ASN J 124 ASN N 12 GLN ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN Q 72 ASN S 68 ASN U 58 ASN V 20 ASN d 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 87845 Z= 0.324 Angle : 0.759 10.692 132342 Z= 0.378 Chirality : 0.041 0.385 17066 Planarity : 0.005 0.068 6406 Dihedral : 19.961 179.415 36132 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 28.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.15), residues: 2608 helix: -1.31 (0.19), residues: 637 sheet: -1.49 (0.26), residues: 392 loop : -2.11 (0.15), residues: 1579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 535 time to evaluate : 3.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 537 average time/residue: 0.7960 time to fit residues: 732.0782 Evaluate side-chains 414 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 3.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 173 optimal weight: 10.0000 chunk 465 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 303 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 517 optimal weight: 20.0000 chunk 429 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 271 optimal weight: 30.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 66 HIS J 96 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 87845 Z= 0.379 Angle : 0.823 10.306 132342 Z= 0.408 Chirality : 0.043 0.499 17066 Planarity : 0.006 0.067 6406 Dihedral : 20.169 179.054 36132 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 31.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.15), residues: 2608 helix: -1.49 (0.18), residues: 654 sheet: -1.67 (0.26), residues: 387 loop : -2.19 (0.15), residues: 1567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 502 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 502 average time/residue: 0.8015 time to fit residues: 691.0761 Evaluate side-chains 390 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 3.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 499 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 435 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 515 optimal weight: 8.9990 chunk 322 optimal weight: 0.0060 chunk 314 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN C 86 ASN D 37 GLN D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 67 GLN G 66 HIS J 96 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN S 60 HIS U 39 ASN U 58 ASN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 87845 Z= 0.211 Angle : 0.661 9.135 132342 Z= 0.333 Chirality : 0.037 0.377 17066 Planarity : 0.005 0.071 6406 Dihedral : 19.715 179.999 36132 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.47 % Favored : 91.49 % Rotamer: Outliers : 0.09 % Allowed : 1.97 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.16), residues: 2608 helix: -1.02 (0.19), residues: 644 sheet: -1.66 (0.24), residues: 438 loop : -1.95 (0.15), residues: 1526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 522 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 523 average time/residue: 0.7931 time to fit residues: 713.1226 Evaluate side-chains 407 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 3.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 319 optimal weight: 4.9990 chunk 205 optimal weight: 20.0000 chunk 307 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 327 optimal weight: 3.9990 chunk 351 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 405 optimal weight: 0.5980 overall best weight: 5.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN D 33 ASN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN G 66 HIS J 96 ASN N 12 GLN P 32 HIS ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS U 58 ASN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 87845 Z= 0.265 Angle : 0.697 9.089 132342 Z= 0.349 Chirality : 0.038 0.366 17066 Planarity : 0.005 0.065 6406 Dihedral : 19.745 179.381 36132 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.01 % Favored : 89.95 % Rotamer: Outliers : 0.04 % Allowed : 1.66 % Favored : 98.30 % 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: -2.53 (0.15), residues: 2608 helix: -1.10 (0.19), residues: 661 sheet: -1.59 (0.24), residues: 434 loop : -2.02 (0.15), residues: 1513 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 504 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 504 average time/residue: 0.7787 time to fit residues: 679.3629 Evaluate side-chains 388 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 469 optimal weight: 0.6980 chunk 494 optimal weight: 10.0000 chunk 450 optimal weight: 0.8980 chunk 480 optimal weight: 6.9990 chunk 493 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 434 optimal weight: 0.9980 chunk 454 optimal weight: 1.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN G 66 HIS J 96 ASN J 124 ASN N 12 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS S 61 ASN U 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 87845 Z= 0.153 Angle : 0.606 9.669 132342 Z= 0.306 Chirality : 0.034 0.352 17066 Planarity : 0.004 0.065 6406 Dihedral : 19.303 179.832 36132 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 0.04 % Allowed : 1.17 % Favored : 98.79 % 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: -2.20 (0.16), residues: 2608 helix: -0.68 (0.20), residues: 657 sheet: -1.38 (0.25), residues: 408 loop : -1.89 (0.15), residues: 1543 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 536 average time/residue: 0.8041 time to fit residues: 737.6567 Evaluate side-chains 406 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 478 optimal weight: 30.0000 chunk 315 optimal weight: 7.9990 chunk 508 optimal weight: 0.0370 chunk 310 optimal weight: 3.9990 chunk 241 optimal weight: 30.0000 chunk 353 optimal weight: 5.9990 chunk 532 optimal weight: 1.9990 chunk 490 optimal weight: 8.9990 chunk 424 optimal weight: 0.0770 chunk 44 optimal weight: 20.0000 chunk 327 optimal weight: 0.2980 overall best weight: 1.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN C 134 ASN D 120 GLN E 67 GLN F 2 ASN G 66 HIS J 96 ASN N 12 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 HIS ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS U 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 87845 Z= 0.137 Angle : 0.580 9.370 132342 Z= 0.292 Chirality : 0.033 0.332 17066 Planarity : 0.004 0.066 6406 Dihedral : 19.017 179.348 36132 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.83 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.98 (0.16), residues: 2608 helix: -0.52 (0.20), residues: 652 sheet: -1.25 (0.25), residues: 408 loop : -1.72 (0.15), residues: 1548 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 551 average time/residue: 0.7848 time to fit residues: 748.0690 Evaluate side-chains 406 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.461 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 260 optimal weight: 10.0000 chunk 337 optimal weight: 0.4980 chunk 452 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 391 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 425 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 436 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 overall best weight: 5.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN D 37 GLN G 66 HIS ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.076285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060412 restraints weight = 349197.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061935 restraints weight = 134318.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062828 restraints weight = 76490.822| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 87845 Z= 0.256 Angle : 0.668 9.038 132342 Z= 0.333 Chirality : 0.036 0.294 17066 Planarity : 0.005 0.069 6406 Dihedral : 19.241 179.177 36132 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.70 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.16), residues: 2608 helix: -0.67 (0.20), residues: 655 sheet: -1.26 (0.25), residues: 411 loop : -1.74 (0.15), residues: 1542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13179.49 seconds wall clock time: 237 minutes 45.88 seconds (14265.88 seconds total)