Starting phenix.real_space_refine on Mon Nov 20 04:06:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/11_2023/7sbb_24976.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/11_2023/7sbb_24976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/11_2023/7sbb_24976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/11_2023/7sbb_24976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/11_2023/7sbb_24976.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/11_2023/7sbb_24976.pdb" } resolution = 3.1 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= 0.015 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: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 113 5.16 5 C 18016 2.51 5 N 4970 2.21 5 O 5764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F ARG 73": "NH1" <-> "NH2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ARG 185": "NH1" <-> "NH2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F GLU 288": "OE1" <-> "OE2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G ARG 185": "NH1" <-> "NH2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G ARG 211": "NH1" <-> "NH2" Residue "G ARG 272": "NH1" <-> "NH2" Residue "H ARG 20": "NH1" <-> "NH2" Residue "H GLU 21": "OE1" <-> "OE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "I GLU 33": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 195": "OE1" <-> "OE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I ARG 496": "NH1" <-> "NH2" Residue "I GLU 513": "OE1" <-> "OE2" Residue "I GLU 515": "OE1" <-> "OE2" Residue "I GLU 613": "OE1" <-> "OE2" Residue "I ARG 616": "NH1" <-> "NH2" Residue "I ARG 631": "NH1" <-> "NH2" Residue "I GLU 667": "OE1" <-> "OE2" Residue "I ARG 680": "NH1" <-> "NH2" Residue "I ARG 710": "NH1" <-> "NH2" Residue "I ARG 717": "NH1" <-> "NH2" Residue "I ARG 774": "NH1" <-> "NH2" Residue "I ARG 801": "NH1" <-> "NH2" Residue "I GLU 803": "OE1" <-> "OE2" Residue "I ARG 805": "NH1" <-> "NH2" Residue "I ARG 807": "NH1" <-> "NH2" Residue "I GLU 870": "OE1" <-> "OE2" Residue "I GLU 882": "OE1" <-> "OE2" Residue "I GLU 883": "OE1" <-> "OE2" Residue "I ARG 898": "NH1" <-> "NH2" Residue "I GLU 900": "OE1" <-> "OE2" Residue "I GLU 921": "OE1" <-> "OE2" Residue "I GLU 939": "OE1" <-> "OE2" Residue "I ARG 952": "NH1" <-> "NH2" Residue "I GLU 960": "OE1" <-> "OE2" Residue "I GLU 969": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J GLU 86": "OE1" <-> "OE2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K ARG 123": "NH1" <-> "NH2" Residue "K GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 28938 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "C" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "E" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "F" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "G" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "H" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Chain: "I" Number of atoms: 5593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5593 Classifications: {'peptide': 680} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 651} Chain breaks: 6 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1194 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "K" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1194 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "X" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 713 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 10} Link IDs: {'rna2p': 5, 'rna3p': 27} Chain: "Z" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 9, 'rna3p_pyr': 14} Link IDs: {'rna2p': 20, 'rna3p': 22} Time building chain proxies: 13.82, per 1000 atoms: 0.48 Number of scatterers: 28938 At special positions: 0 Unit cell: (114.95, 123.31, 229.9, 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 113 16.00 P 75 15.00 O 5764 8.00 N 4970 7.00 C 18016 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: 10.57 Conformation dependent library (CDL) restraints added in 4.5 seconds 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6424 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 34 sheets defined 46.5% alpha, 15.9% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 8.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 64 through 83 Proline residue: A 71 - end of helix removed outlier: 3.724A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.656A pdb=" N THR A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.538A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 317 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.515A pdb=" N THR B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.732A pdb=" N GLN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 317 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.887A pdb=" N GLN C 68 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.891A pdb=" N ASP C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 Processing helix chain 'C' and resid 295 through 317 removed outlier: 3.516A pdb=" N GLY C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 64 through 68 removed outlier: 3.976A pdb=" N GLN D 68 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 83 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 137 through 140 Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.578A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 295 through 317 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 64 through 83 removed outlier: 3.926A pdb=" N GLN E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Proline residue: E 71 - end of helix removed outlier: 3.651A pdb=" N ALA E 75 " --> pdb=" O PRO E 71 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 231 through 244 Processing helix chain 'E' and resid 250 through 267 Processing helix chain 'E' and resid 279 through 294 removed outlier: 3.771A pdb=" N GLN E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 317 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 69 through 83 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 137 through 140 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 279 through 290 removed outlier: 3.938A pdb=" N THR F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 317 removed outlier: 3.599A pdb=" N LEU F 299 " --> pdb=" O ASN F 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.514A pdb=" N LYS G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 69 through 83 removed outlier: 3.602A pdb=" N LEU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.631A pdb=" N THR G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 removed outlier: 3.935A pdb=" N THR G 236 " --> pdb=" O ASN G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 266 removed outlier: 3.518A pdb=" N LEU G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA G 259 " --> pdb=" O CYS G 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 260 " --> pdb=" O GLU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 293 removed outlier: 3.940A pdb=" N THR G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU G 288 " --> pdb=" O THR G 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 317 removed outlier: 4.513A pdb=" N LYS G 301 " --> pdb=" O ALA G 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 43 Processing helix chain 'H' and resid 54 through 59 removed outlier: 4.068A pdb=" N ASN H 57 " --> pdb=" O VAL H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 79 removed outlier: 3.617A pdb=" N ASN H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.182A pdb=" N ARG I 11 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU I 13 " --> pdb=" O LEU I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 27 through 36 removed outlier: 4.258A pdb=" N ALA I 31 " --> pdb=" O THR I 27 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU I 34 " --> pdb=" O PRO I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 96 removed outlier: 3.632A pdb=" N GLU I 95 " --> pdb=" O ASN I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.748A pdb=" N ARG I 106 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU I 107 " --> pdb=" O ILE I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 148 removed outlier: 3.715A pdb=" N ASN I 139 " --> pdb=" O GLN I 135 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 140 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 146 " --> pdb=" O LEU I 142 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG I 147 " --> pdb=" O GLU I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 154 removed outlier: 3.649A pdb=" N PHE I 153 " --> pdb=" O ASN I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 159 removed outlier: 4.030A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 removed outlier: 3.525A pdb=" N ALA I 168 " --> pdb=" O ILE I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 213 removed outlier: 4.021A pdb=" N ASP I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 201 - end of helix removed outlier: 3.569A pdb=" N HIS I 204 " --> pdb=" O HIS I 200 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP I 210 " --> pdb=" O LEU I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 222 removed outlier: 3.804A pdb=" N LEU I 221 " --> pdb=" O PRO I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 238 removed outlier: 6.364A pdb=" N ARG I 229 " --> pdb=" O THR I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 269 removed outlier: 3.712A pdb=" N ASN I 257 " --> pdb=" O GLY I 253 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 316 removed outlier: 3.877A pdb=" N GLN I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 497 removed outlier: 3.807A pdb=" N ASP I 492 " --> pdb=" O GLN I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 518 removed outlier: 3.705A pdb=" N ILE I 511 " --> pdb=" O HIS I 507 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN I 512 " --> pdb=" O GLN I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 584 Processing helix chain 'I' and resid 590 through 595 Processing helix chain 'I' and resid 608 through 620 removed outlier: 3.638A pdb=" N GLU I 613 " --> pdb=" O PRO I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 626 through 636 removed outlier: 3.569A pdb=" N VAL I 630 " --> pdb=" O ASN I 626 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS I 632 " --> pdb=" O TRP I 628 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP I 634 " --> pdb=" O VAL I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 647 removed outlier: 3.568A pdb=" N LEU I 647 " --> pdb=" O LEU I 644 " (cutoff:3.500A) Processing helix chain 'I' and resid 683 through 703 removed outlier: 4.815A pdb=" N LYS I 690 " --> pdb=" O ASP I 686 " (cutoff:3.500A) Proline residue: I 691 - end of helix Proline residue: I 699 - end of helix Processing helix chain 'I' and resid 720 through 724 removed outlier: 3.924A pdb=" N GLU I 724 " --> pdb=" O ASP I 721 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 739 removed outlier: 4.249A pdb=" N SER I 736 " --> pdb=" O ALA I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 745 through 747 No H-bonds generated for 'chain 'I' and resid 745 through 747' Processing helix chain 'I' and resid 748 through 764 Processing helix chain 'I' and resid 774 through 776 No H-bonds generated for 'chain 'I' and resid 774 through 776' Processing helix chain 'I' and resid 777 through 788 Processing helix chain 'I' and resid 790 through 803 Processing helix chain 'I' and resid 809 through 824 removed outlier: 3.942A pdb=" N THR I 814 " --> pdb=" O GLU I 810 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP I 817 " --> pdb=" O VAL I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 827 through 845 removed outlier: 3.643A pdb=" N VAL I 841 " --> pdb=" O THR I 837 " (cutoff:3.500A) Processing helix chain 'I' and resid 851 through 855 Processing helix chain 'I' and resid 857 through 862 Processing helix chain 'I' and resid 862 through 875 Processing helix chain 'I' and resid 880 through 897 removed outlier: 4.368A pdb=" N LEU I 886 " --> pdb=" O GLU I 882 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 899 No H-bonds generated for 'chain 'I' and resid 898 through 899' Processing helix chain 'I' and resid 900 through 903 Processing helix chain 'I' and resid 904 through 909 removed outlier: 4.318A pdb=" N ASP I 909 " --> pdb=" O PRO I 905 " (cutoff:3.500A) Processing helix chain 'I' and resid 913 through 935 Processing helix chain 'I' and resid 944 through 974 removed outlier: 5.007A pdb=" N ASN I 953 " --> pdb=" O GLN I 949 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG I 954 " --> pdb=" O GLU I 950 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 removed outlier: 4.443A pdb=" N LYS J 4 " --> pdb=" O MET J 1 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 17 removed outlier: 3.648A pdb=" N TYR J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 26 Processing helix chain 'J' and resid 28 through 33 Processing helix chain 'J' and resid 33 through 46 Processing helix chain 'J' and resid 51 through 68 removed outlier: 3.907A pdb=" N LEU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU J 57 " --> pdb=" O GLU J 53 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA J 66 " --> pdb=" O GLN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 84 through 105 Processing helix chain 'J' and resid 115 through 122 removed outlier: 3.504A pdb=" N GLN J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 145 removed outlier: 3.704A pdb=" N GLN J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 17 removed outlier: 5.257A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL K 12 " --> pdb=" O THR K 8 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 26 Processing helix chain 'K' and resid 28 through 33 Processing helix chain 'K' and resid 33 through 45 Processing helix chain 'K' and resid 51 through 68 Processing helix chain 'K' and resid 71 through 74 Processing helix chain 'K' and resid 75 through 80 Processing helix chain 'K' and resid 84 through 106 Processing helix chain 'K' and resid 115 through 121 Processing helix chain 'K' and resid 122 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.243A pdb=" N LEU A 27 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A 219 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N HIS A 29 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN A 217 " --> pdb=" O HIS A 29 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN A 31 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET A 215 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 275 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.665A pdb=" N THR A 38 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.011A pdb=" N GLY A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 128 removed outlier: 6.915A pdb=" N TYR B 21 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B 224 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS B 23 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 222 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 25 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR B 214 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 275 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.837A pdb=" N THR B 38 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 48 Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 148 Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.939A pdb=" N TYR C 21 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 224 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS C 23 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 222 " --> pdb=" O HIS C 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 25 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 214 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU C 275 " --> pdb=" O PHE C 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.818A pdb=" N THR C 38 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 44 through 48 Processing sheet with id=AB6, first strand: chain 'C' and resid 142 through 148 Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 128 removed outlier: 6.937A pdb=" N TYR D 21 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE D 224 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS D 23 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE D 222 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 25 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 275 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 48 Processing sheet with id=AB9, first strand: chain 'D' and resid 142 through 148 Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 128 removed outlier: 6.489A pdb=" N LEU E 27 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU E 219 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HIS E 29 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASN E 217 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 142 through 148 Processing sheet with id=AC4, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.492A pdb=" N LEU F 27 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU F 219 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N HIS F 29 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN F 217 " --> pdb=" O HIS F 29 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU F 275 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 44 through 48 Processing sheet with id=AC6, first strand: chain 'F' and resid 142 through 147 removed outlier: 4.456A pdb=" N ASN F 167 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 127 through 129 removed outlier: 6.534A pdb=" N LEU G 27 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU G 219 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS G 29 " --> pdb=" O ASN G 217 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN G 217 " --> pdb=" O HIS G 29 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU G 275 " --> pdb=" O PHE G 224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 44 through 47 removed outlier: 6.549A pdb=" N SER G 59 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 136 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU G 61 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 142 through 146 Processing sheet with id=AD1, first strand: chain 'H' and resid 80 through 82 removed outlier: 6.656A pdb=" N GLU H 135 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AD3, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AD4, first strand: chain 'H' and resid 174 through 182 removed outlier: 5.566A pdb=" N PHE H 211 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL H 203 " --> pdb=" O PHE H 211 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 213 " --> pdb=" O ASN H 201 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN H 217 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE H 197 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASP H 219 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN H 195 " --> pdb=" O ASP H 219 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 174 through 182 removed outlier: 5.976A pdb=" N GLN H 222 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU H 229 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP H 224 " --> pdb=" O THR H 227 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 273 through 278 removed outlier: 6.863A pdb=" N ILE I 283 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE I 277 " --> pdb=" O GLY I 281 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY I 281 " --> pdb=" O PHE I 277 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 673 through 677 removed outlier: 3.744A pdb=" N ALA I 673 " --> pdb=" O LEU I 601 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE I 597 " --> pdb=" O THR I 677 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 10.11 Time building geometry restraints manager: 11.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4705 1.28 - 1.42: 8082 1.42 - 1.55: 16491 1.55 - 1.69: 202 1.69 - 1.82: 180 Bond restraints: 29660 Sorted by residual: bond pdb=" C TYR E 313 " pdb=" O TYR E 313 " ideal model delta sigma weight residual 1.237 1.143 0.094 1.17e-02 7.31e+03 6.39e+01 bond pdb=" C TYR F 313 " pdb=" O TYR F 313 " ideal model delta sigma weight residual 1.236 1.146 0.091 1.15e-02 7.56e+03 6.21e+01 bond pdb=" C TYR D 313 " pdb=" O TYR D 313 " ideal model delta sigma weight residual 1.237 1.145 0.091 1.16e-02 7.43e+03 6.21e+01 bond pdb=" C TYR C 313 " pdb=" O TYR C 313 " ideal model delta sigma weight residual 1.237 1.150 0.087 1.17e-02 7.31e+03 5.49e+01 bond pdb=" CA ASN H 71 " pdb=" C ASN H 71 " ideal model delta sigma weight residual 1.522 1.435 0.087 1.21e-02 6.83e+03 5.12e+01 ... (remaining 29655 not shown) Histogram of bond angle deviations from ideal: 91.34 - 100.17: 63 100.17 - 109.00: 4425 109.00 - 117.83: 16667 117.83 - 126.65: 18688 126.65 - 135.48: 624 Bond angle restraints: 40467 Sorted by residual: angle pdb=" N PHE I 285 " pdb=" CA PHE I 285 " pdb=" C PHE I 285 " ideal model delta sigma weight residual 110.32 91.34 18.98 1.59e+00 3.96e-01 1.42e+02 angle pdb=" CA ASP F 130 " pdb=" CB ASP F 130 " pdb=" CG ASP F 130 " ideal model delta sigma weight residual 112.60 122.48 -9.88 1.00e+00 1.00e+00 9.77e+01 angle pdb=" N GLY G 114 " pdb=" CA GLY G 114 " pdb=" C GLY G 114 " ideal model delta sigma weight residual 112.29 123.12 -10.83 1.12e+00 7.97e-01 9.36e+01 angle pdb=" CA ASP I 640 " pdb=" CB ASP I 640 " pdb=" CG ASP I 640 " ideal model delta sigma weight residual 112.60 122.23 -9.63 1.00e+00 1.00e+00 9.26e+01 angle pdb=" CA ASP A 130 " pdb=" CB ASP A 130 " pdb=" CG ASP A 130 " ideal model delta sigma weight residual 112.60 121.67 -9.07 1.00e+00 1.00e+00 8.22e+01 ... (remaining 40462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 17125 35.55 - 71.11: 476 71.11 - 106.66: 77 106.66 - 142.22: 6 142.22 - 177.77: 3 Dihedral angle restraints: 17687 sinusoidal: 7708 harmonic: 9979 Sorted by residual: dihedral pdb=" O4' U Z 3 " pdb=" C1' U Z 3 " pdb=" N1 U Z 3 " pdb=" C2 U Z 3 " ideal model delta sinusoidal sigma weight residual -160.00 -0.90 -159.10 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U Z 34 " pdb=" C1' U Z 34 " pdb=" N1 U Z 34 " pdb=" C2 U Z 34 " ideal model delta sinusoidal sigma weight residual 200.00 62.15 137.85 1 1.50e+01 4.44e-03 7.43e+01 dihedral pdb=" O4' U Z 35 " pdb=" C1' U Z 35 " pdb=" N1 U Z 35 " pdb=" C2 U Z 35 " ideal model delta sinusoidal sigma weight residual 200.00 73.45 126.55 1 1.50e+01 4.44e-03 6.81e+01 ... (remaining 17684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 3643 0.157 - 0.313: 765 0.313 - 0.470: 117 0.470 - 0.627: 29 0.627 - 0.784: 11 Chirality restraints: 4565 Sorted by residual: chirality pdb=" CA GLU A 228 " pdb=" N GLU A 228 " pdb=" C GLU A 228 " pdb=" CB GLU A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA GLU A 288 " pdb=" N GLU A 288 " pdb=" C GLU A 288 " pdb=" CB GLU A 288 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA GLU I 812 " pdb=" N GLU I 812 " pdb=" C GLU I 812 " pdb=" CB GLU I 812 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 4562 not shown) Planarity restraints: 4974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G Z 25 " -0.025 2.00e-02 2.50e+03 1.16e-01 4.01e+02 pdb=" N9 G Z 25 " -0.067 2.00e-02 2.50e+03 pdb=" C8 G Z 25 " 0.150 2.00e-02 2.50e+03 pdb=" N7 G Z 25 " 0.149 2.00e-02 2.50e+03 pdb=" C5 G Z 25 " -0.019 2.00e-02 2.50e+03 pdb=" C6 G Z 25 " -0.052 2.00e-02 2.50e+03 pdb=" O6 G Z 25 " -0.067 2.00e-02 2.50e+03 pdb=" N1 G Z 25 " -0.017 2.00e-02 2.50e+03 pdb=" C2 G Z 25 " -0.055 2.00e-02 2.50e+03 pdb=" N2 G Z 25 " 0.258 2.00e-02 2.50e+03 pdb=" N3 G Z 25 " -0.147 2.00e-02 2.50e+03 pdb=" C4 G Z 25 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U Z 34 " -0.263 2.00e-02 2.50e+03 1.28e-01 3.70e+02 pdb=" N1 U Z 34 " 0.058 2.00e-02 2.50e+03 pdb=" C2 U Z 34 " 0.047 2.00e-02 2.50e+03 pdb=" O2 U Z 34 " 0.102 2.00e-02 2.50e+03 pdb=" N3 U Z 34 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U Z 34 " -0.015 2.00e-02 2.50e+03 pdb=" O4 U Z 34 " -0.179 2.00e-02 2.50e+03 pdb=" C5 U Z 34 " 0.114 2.00e-02 2.50e+03 pdb=" C6 U Z 34 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 584 " 0.189 2.00e-02 2.50e+03 1.18e-01 3.46e+02 pdb=" CG TRP I 584 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP I 584 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TRP I 584 " -0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP I 584 " -0.115 2.00e-02 2.50e+03 pdb=" CE2 TRP I 584 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP I 584 " -0.166 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 584 " 0.143 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 584 " -0.090 2.00e-02 2.50e+03 pdb=" CH2 TRP I 584 " 0.153 2.00e-02 2.50e+03 ... (remaining 4971 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 148 2.60 - 3.18: 23739 3.18 - 3.75: 46863 3.75 - 4.33: 66230 4.33 - 4.90: 107426 Nonbonded interactions: 244406 Sorted by model distance: nonbonded pdb=" CB SER E 144 " pdb=" OD1 ASP E 170 " model vdw 2.030 3.440 nonbonded pdb=" CG MET D 162 " pdb=" O2' A X 10 " model vdw 2.161 3.440 nonbonded pdb=" NE2 GLN G 8 " pdb=" OE1 GLU G 275 " model vdw 2.188 2.520 nonbonded pdb=" O LEU E 302 " pdb=" OG SER E 305 " model vdw 2.213 2.440 nonbonded pdb=" N PHE I 285 " pdb=" O PHE I 285 " model vdw 2.226 2.496 ... (remaining 244401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.00 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: 3.870 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: 0.020 Extract box with map and model: 18.710 Check model and map are aligned: 0.380 Set scattering table: 0.280 Process input model: 74.100 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.013 0.094 29660 Z= 0.844 Angle : 2.086 18.976 40467 Z= 1.376 Chirality : 0.139 0.784 4565 Planarity : 0.021 0.251 4974 Dihedral : 17.084 177.772 11263 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.65 % Favored : 95.20 % Rotamer: Outliers : 3.53 % Allowed : 7.88 % Favored : 88.59 % Cbeta Deviations : 3.02 % Peptide Plane: Cis-proline : 0.85 % 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: -2.12 (0.13), residues: 3399 helix: -1.94 (0.11), residues: 1445 sheet: -0.42 (0.23), residues: 377 loop : -0.94 (0.15), residues: 1577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1148 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 28 residues processed: 1197 average time/residue: 0.4847 time to fit residues: 867.5389 Evaluate side-chains 991 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 963 time to evaluate : 3.412 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3493 time to fit residues: 20.8164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 0.7980 chunk 264 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 273 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 166 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 316 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 198 ASN A 218 HIS A 295 ASN B 43 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 106 GLN B 148 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 242 GLN B 309 GLN C 43 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 281 HIS ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 208 GLN D 267 ASN D 308 GLN E 8 GLN E 48 GLN E 68 GLN E 82 ASN E 106 GLN E 140 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN E 208 GLN E 232 ASN E 242 GLN E 294 GLN F 43 ASN F 48 GLN F 106 GLN F 198 ASN F 242 GLN G 10 GLN G 20 HIS H 49 HIS H 70 GLN H 95 ASN H 143 GLN I 81 HIS I 84 ASN I 219 HIS I 235 ASN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 GLN I 488 GLN I 636 ASN I 651 ASN I 754 ASN I 849 GLN ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 891 GLN I 918 GLN I 951 GLN J 62 GLN J 143 GLN J 146 ASN K 89 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29660 Z= 0.283 Angle : 0.794 10.162 40467 Z= 0.416 Chirality : 0.049 0.416 4565 Planarity : 0.005 0.085 4974 Dihedral : 12.627 177.662 4648 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 3.33 % Allowed : 15.15 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.72 (0.14), residues: 3399 helix: -0.10 (0.13), residues: 1498 sheet: 0.04 (0.24), residues: 393 loop : -0.89 (0.16), residues: 1508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 988 time to evaluate : 3.094 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 outliers start: 99 outliers final: 49 residues processed: 1023 average time/residue: 0.4782 time to fit residues: 734.2024 Evaluate side-chains 985 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 936 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3158 time to fit residues: 31.2039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 176 optimal weight: 0.0060 chunk 98 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 317 optimal weight: 1.9990 chunk 342 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 254 optimal weight: 9.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN B 8 GLN B 43 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 295 ASN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN F 43 ASN F 167 ASN F 198 ASN F 263 GLN G 106 GLN H 95 ASN ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 918 GLN ** I 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN K 70 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29660 Z= 0.352 Angle : 0.730 10.020 40467 Z= 0.381 Chirality : 0.048 0.377 4565 Planarity : 0.005 0.065 4974 Dihedral : 12.286 179.118 4648 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.00 % Allowed : 18.11 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3399 helix: 0.43 (0.13), residues: 1495 sheet: -0.05 (0.23), residues: 418 loop : -0.93 (0.16), residues: 1486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 971 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 51 residues processed: 999 average time/residue: 0.4920 time to fit residues: 743.2413 Evaluate side-chains 996 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 945 time to evaluate : 3.118 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2952 time to fit residues: 32.0153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 318 optimal weight: 0.9980 chunk 337 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 301 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 171 HIS D 295 ASN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 198 ASN G 10 GLN H 95 ASN H 217 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 661 GLN ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN J 58 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.005 0.055 29660 Z= 0.328 Angle : 0.698 9.632 40467 Z= 0.364 Chirality : 0.047 0.401 4565 Planarity : 0.005 0.058 4974 Dihedral : 12.160 179.922 4648 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.73 % Allowed : 19.66 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3399 helix: 0.70 (0.14), residues: 1494 sheet: -0.09 (0.23), residues: 412 loop : -0.99 (0.16), residues: 1493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 970 time to evaluate : 3.514 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 outliers start: 81 outliers final: 45 residues processed: 998 average time/residue: 0.4900 time to fit residues: 740.4144 Evaluate side-chains 997 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 952 time to evaluate : 3.114 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3036 time to fit residues: 28.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 287 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 302 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 167 ASN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 295 ASN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 217 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 288 GLN I 581 GLN I 818 GLN ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 29660 Z= 0.311 Angle : 0.687 9.617 40467 Z= 0.357 Chirality : 0.046 0.380 4565 Planarity : 0.004 0.058 4974 Dihedral : 12.061 179.744 4648 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.05 % Allowed : 21.98 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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 (0.14), residues: 3399 helix: 0.82 (0.14), residues: 1502 sheet: 0.06 (0.23), residues: 422 loop : -1.04 (0.16), residues: 1475 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 956 time to evaluate : 3.297 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 outliers start: 61 outliers final: 25 residues processed: 973 average time/residue: 0.4831 time to fit residues: 706.8678 Evaluate side-chains 967 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 942 time to evaluate : 3.113 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2955 time to fit residues: 17.7428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 0.9980 chunk 303 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 337 optimal weight: 0.6980 chunk 280 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 177 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 217 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 295 ASN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 GLN H 95 ASN H 217 GLN H 231 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN J 64 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29660 Z= 0.249 Angle : 0.668 13.360 40467 Z= 0.344 Chirality : 0.044 0.374 4565 Planarity : 0.004 0.052 4974 Dihedral : 11.970 179.924 4648 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.22 % Allowed : 23.26 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: -0.07 (0.14), residues: 3399 helix: 0.96 (0.14), residues: 1502 sheet: -0.08 (0.22), residues: 441 loop : -1.07 (0.16), residues: 1456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 948 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 46 residues processed: 965 average time/residue: 0.5071 time to fit residues: 743.8085 Evaluate side-chains 987 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 941 time to evaluate : 3.321 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3284 time to fit residues: 30.7089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 325 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 336 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN D 68 GLN D 99 ASN D 295 ASN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 217 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29660 Z= 0.355 Angle : 0.707 11.204 40467 Z= 0.366 Chirality : 0.047 0.367 4565 Planarity : 0.005 0.083 4974 Dihedral : 11.932 179.098 4648 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.82 % Allowed : 24.44 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: -0.04 (0.14), residues: 3399 helix: 1.06 (0.14), residues: 1473 sheet: -0.11 (0.22), residues: 429 loop : -1.08 (0.16), residues: 1497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 947 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 35 residues processed: 964 average time/residue: 0.5011 time to fit residues: 734.3885 Evaluate side-chains 962 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 927 time to evaluate : 2.824 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3287 time to fit residues: 23.7902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 208 optimal weight: 40.0000 chunk 134 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 229 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 264 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 68 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN H 95 ASN H 217 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 951 GLN J 97 GLN K 30 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29660 Z= 0.292 Angle : 0.699 10.137 40467 Z= 0.361 Chirality : 0.045 0.358 4565 Planarity : 0.004 0.054 4974 Dihedral : 11.899 179.271 4648 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.68 % Allowed : 25.31 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.02 (0.14), residues: 3399 helix: 1.12 (0.14), residues: 1476 sheet: -0.05 (0.23), residues: 415 loop : -1.07 (0.15), residues: 1508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 944 time to evaluate : 3.266 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 outliers start: 50 outliers final: 33 residues processed: 957 average time/residue: 0.4856 time to fit residues: 703.4000 Evaluate side-chains 949 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 916 time to evaluate : 3.437 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3061 time to fit residues: 22.4890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 305 optimal weight: 0.9990 chunk 322 optimal weight: 0.0970 chunk 294 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 246 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 312 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 217 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN D 31 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 217 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 GLN I 581 GLN ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29660 Z= 0.298 Angle : 0.704 11.762 40467 Z= 0.361 Chirality : 0.045 0.350 4565 Planarity : 0.004 0.051 4974 Dihedral : 11.845 178.983 4648 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.21 % Allowed : 26.15 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.02 (0.14), residues: 3399 helix: 1.12 (0.14), residues: 1476 sheet: -0.05 (0.23), residues: 410 loop : -1.07 (0.15), residues: 1513 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 956 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 963 average time/residue: 0.4841 time to fit residues: 705.9154 Evaluate side-chains 969 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 944 time to evaluate : 3.243 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2890 time to fit residues: 18.0041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 205 optimal weight: 2.9990 chunk 331 optimal weight: 0.7980 chunk 202 optimal weight: 0.1980 chunk 157 optimal weight: 0.7980 chunk 230 optimal weight: 0.6980 chunk 347 optimal weight: 0.9990 chunk 320 optimal weight: 1.9990 chunk 276 optimal weight: 0.0000 chunk 28 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 217 ASN D 295 ASN D 309 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 198 ASN G 309 GLN H 95 ASN H 217 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 581 GLN ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29660 Z= 0.240 Angle : 0.700 12.727 40467 Z= 0.358 Chirality : 0.044 0.339 4565 Planarity : 0.004 0.082 4974 Dihedral : 11.818 179.478 4648 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.77 % Allowed : 27.57 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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 (0.14), residues: 3399 helix: 1.18 (0.14), residues: 1479 sheet: -0.02 (0.23), residues: 408 loop : -1.06 (0.15), residues: 1512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 961 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 965 average time/residue: 0.4960 time to fit residues: 726.1008 Evaluate side-chains 977 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 963 time to evaluate : 3.477 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4194 time to fit residues: 14.5347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 219 optimal weight: 0.5980 chunk 294 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 255 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 284 optimal weight: 0.7980 chunk 35 optimal weight: 0.0020 chunk 51 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN D 68 GLN D 295 ASN D 309 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 GLN F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN H 95 ASN H 217 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 GLN ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114107 restraints weight = 43906.315| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.01 r_work: 0.3340 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29660 Z= 0.259 Angle : 0.703 14.739 40467 Z= 0.358 Chirality : 0.044 0.333 4565 Planarity : 0.004 0.063 4974 Dihedral : 11.779 179.665 4648 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.57 % Allowed : 27.80 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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 (0.14), residues: 3399 helix: 1.18 (0.14), residues: 1477 sheet: -0.03 (0.23), residues: 408 loop : -1.07 (0.15), residues: 1514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11250.64 seconds wall clock time: 201 minutes 41.94 seconds (12101.94 seconds total)