Starting phenix.real_space_refine (version: dev) on Sun Dec 18 19:58:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr8_26082/12_2022/7tr8_26082.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr8_26082/12_2022/7tr8_26082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr8_26082/12_2022/7tr8_26082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr8_26082/12_2022/7tr8_26082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr8_26082/12_2022/7tr8_26082.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr8_26082/12_2022/7tr8_26082.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "I TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "K PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 117": "OD1" <-> "OD2" Residue "N TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 316": "OD1" <-> "OD2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 33581 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4307 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2494 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2134 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1823 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain: "R" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 949 Classifications: {'RNA': 45} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna2p': 18, 'rna3p': 26} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.85, per 1000 atoms: 0.53 Number of scatterers: 33581 At special positions: 0 Unit cell: (117.619, 153.558, 218.902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 S 80 16.00 P 44 15.00 O 6374 8.00 N 5740 7.00 C 21341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 65 " distance=2.03 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: 14.53 Conformation dependent library (CDL) restraints added in 4.9 seconds 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7808 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 45 sheets defined 39.8% alpha, 11.2% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 10.27 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.079A pdb=" N ARG A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 29' Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 78 through 95 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 133 through 140 Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.639A pdb=" N ALA A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 243 through 255 removed outlier: 4.511A pdb=" N ASP A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 280 removed outlier: 3.616A pdb=" N ASN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.566A pdb=" N GLN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.733A pdb=" N ALA A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 removed outlier: 4.024A pdb=" N THR A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.886A pdb=" N GLY A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.764A pdb=" N ILE A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.679A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.588A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'C' and resid 13 through 30 removed outlier: 4.260A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 71 removed outlier: 3.634A pdb=" N ALA C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 116 removed outlier: 3.708A pdb=" N TRP C 100 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 3.525A pdb=" N LYS C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.960A pdb=" N LEU C 218 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 219 " --> pdb=" O ASP C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 219' Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.937A pdb=" N HIS C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.946A pdb=" N LYS C 287 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 288 " --> pdb=" O HIS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 310 Processing helix chain 'C' and resid 311 through 326 removed outlier: 4.346A pdb=" N PHE C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.611A pdb=" N VAL C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 13 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.891A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.749A pdb=" N GLU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 100 removed outlier: 3.971A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER D 96 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.840A pdb=" N ASN E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 removed outlier: 4.028A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 50 through 59 removed outlier: 3.962A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 70 through 83 Processing helix chain 'E' and resid 86 through 100 removed outlier: 3.849A pdb=" N LYS E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 removed outlier: 3.606A pdb=" N TYR F 11 " --> pdb=" O ASN F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 24 through 34 removed outlier: 4.340A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 49 Processing helix chain 'F' and resid 50 through 59 removed outlier: 4.186A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 removed outlier: 3.663A pdb=" N ILE F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 100 removed outlier: 3.518A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'G' and resid 5 through 14 removed outlier: 3.803A pdb=" N TYR G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.899A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.703A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 57 removed outlier: 3.784A pdb=" N LEU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.742A pdb=" N GLY G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 83 removed outlier: 4.098A pdb=" N ILE G 74 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU G 75 " --> pdb=" O PRO G 71 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.563A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 14 Processing helix chain 'H' and resid 24 through 33 removed outlier: 4.339A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA H 32 " --> pdb=" O VAL H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.675A pdb=" N LEU H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 removed outlier: 4.147A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 4.041A pdb=" N GLU H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 102 removed outlier: 3.510A pdb=" N LEU H 90 " --> pdb=" O ASN H 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 removed outlier: 3.793A pdb=" N LEU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 removed outlier: 4.326A pdb=" N VAL I 74 " --> pdb=" O PRO I 71 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN I 75 " --> pdb=" O TYR I 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 71 through 75' Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.782A pdb=" N LEU I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 82' Processing helix chain 'I' and resid 107 through 115 Processing helix chain 'I' and resid 116 through 122 Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 285 through 300 Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.786A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 75 removed outlier: 4.419A pdb=" N VAL J 74 " --> pdb=" O PRO J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.510A pdb=" N LEU J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'J' and resid 107 through 115 Processing helix chain 'J' and resid 116 through 121 Processing helix chain 'J' and resid 144 through 152 Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 242 through 243 No H-bonds generated for 'chain 'J' and resid 242 through 243' Processing helix chain 'J' and resid 244 through 248 removed outlier: 3.640A pdb=" N SER J 247 " --> pdb=" O PRO J 244 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY J 248 " --> pdb=" O MET J 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 244 through 248' Processing helix chain 'J' and resid 285 through 300 removed outlier: 3.558A pdb=" N ALA J 289 " --> pdb=" O ASP J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 335 removed outlier: 3.634A pdb=" N MET J 335 " --> pdb=" O ASN J 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 69 removed outlier: 3.679A pdb=" N LEU K 55 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 removed outlier: 4.232A pdb=" N VAL K 74 " --> pdb=" O PRO K 71 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN K 75 " --> pdb=" O TYR K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 324 through 335 Processing helix chain 'L' and resid 51 through 69 removed outlier: 3.617A pdb=" N LYS L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.635A pdb=" N LEU L 81 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 77 through 82' Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 115 through 122 Processing helix chain 'L' and resid 144 through 152 removed outlier: 3.565A pdb=" N GLU L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.618A pdb=" N MET L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 299 removed outlier: 3.742A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA L 299 " --> pdb=" O LYS L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 333 removed outlier: 3.631A pdb=" N LEU L 328 " --> pdb=" O SER L 324 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL L 329 " --> pdb=" O VAL L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'M' and resid 20 through 24 removed outlier: 3.621A pdb=" N THR M 24 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.936A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 75 removed outlier: 4.023A pdb=" N VAL M 74 " --> pdb=" O PRO M 71 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN M 75 " --> pdb=" O TYR M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 3.556A pdb=" N LEU M 81 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 77 through 82' Processing helix chain 'M' and resid 107 through 115 removed outlier: 3.548A pdb=" N LYS M 113 " --> pdb=" O ALA M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 122 removed outlier: 3.531A pdb=" N ASP M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 246 removed outlier: 3.778A pdb=" N LEU M 246 " --> pdb=" O ILE M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 300 removed outlier: 3.805A pdb=" N ALA M 289 " --> pdb=" O ASP M 285 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA M 297 " --> pdb=" O ILE M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 334 Processing helix chain 'N' and resid 51 through 70 removed outlier: 3.727A pdb=" N LEU N 55 " --> pdb=" O THR N 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR N 70 " --> pdb=" O TYR N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 Processing helix chain 'N' and resid 107 through 115 removed outlier: 3.531A pdb=" N ILE N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 122 removed outlier: 4.192A pdb=" N VAL N 120 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS N 121 " --> pdb=" O ASP N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 150 removed outlier: 3.708A pdb=" N GLU N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 155 No H-bonds generated for 'chain 'N' and resid 153 through 155' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 285 through 301 removed outlier: 3.608A pdb=" N ALA N 297 " --> pdb=" O ILE N 293 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY N 301 " --> pdb=" O ALA N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.647A pdb=" N LEU N 328 " --> pdb=" O SER N 324 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 69 removed outlier: 3.732A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 Processing helix chain 'O' and resid 107 through 113 removed outlier: 3.534A pdb=" N LYS O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 121 removed outlier: 3.583A pdb=" N VAL O 120 " --> pdb=" O ALA O 116 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS O 121 " --> pdb=" O ASP O 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 116 through 121' Processing helix chain 'O' and resid 144 through 150 removed outlier: 3.629A pdb=" N GLU O 150 " --> pdb=" O ASP O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 285 through 299 removed outlier: 3.544A pdb=" N ALA O 289 " --> pdb=" O ASP O 285 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA O 297 " --> pdb=" O ILE O 293 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA O 299 " --> pdb=" O LYS O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 335 removed outlier: 4.008A pdb=" N MET O 335 " --> pdb=" O ASN O 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 46 Processing helix chain 'P' and resid 54 through 69 Processing helix chain 'P' and resid 129 through 141 removed outlier: 3.601A pdb=" N ASN P 134 " --> pdb=" O GLN P 130 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 182 removed outlier: 3.857A pdb=" N SER P 181 " --> pdb=" O GLU P 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 24 removed outlier: 3.944A pdb=" N ILE Q 24 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 38 Proline residue: Q 31 - end of helix removed outlier: 3.544A pdb=" N ARG Q 35 " --> pdb=" O PRO Q 31 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL Q 36 " --> pdb=" O SER Q 32 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET Q 37 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS Q 38 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 59 Processing helix chain 'Q' and resid 62 through 66 removed outlier: 3.500A pdb=" N CYS Q 65 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER Q 66 " --> pdb=" O GLY Q 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 66' Processing helix chain 'Q' and resid 68 through 73 Processing helix chain 'Q' and resid 84 through 101 removed outlier: 3.756A pdb=" N SER Q 88 " --> pdb=" O HIS Q 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Q 89 " --> pdb=" O GLU Q 85 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR Q 90 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS Q 97 " --> pdb=" O TYR Q 93 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP Q 98 " --> pdb=" O ASN Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.935A pdb=" N ALA Q 106 " --> pdb=" O ASP Q 102 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 143 removed outlier: 3.598A pdb=" N VAL Q 138 " --> pdb=" O THR Q 134 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP Q 140 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 158 removed outlier: 4.300A pdb=" N GLU Q 153 " --> pdb=" O MET Q 149 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER Q 154 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS Q 157 " --> pdb=" O GLU Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 164 removed outlier: 3.554A pdb=" N LYS Q 163 " --> pdb=" O MET Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 192 removed outlier: 4.079A pdb=" N VAL Q 178 " --> pdb=" O THR Q 174 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU Q 179 " --> pdb=" O GLN Q 175 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 210 removed outlier: 3.659A pdb=" N LEU Q 198 " --> pdb=" O ASP Q 194 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG Q 199 " --> pdb=" O SER Q 195 " (cutoff:3.500A) Proline residue: Q 208 - end of helix Processing helix chain 'Q' and resid 211 through 216 removed outlier: 4.011A pdb=" N GLY Q 215 " --> pdb=" O CYS Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 227 removed outlier: 3.909A pdb=" N ALA Q 226 " --> pdb=" O ALA Q 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.527A pdb=" N VAL A 162 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET A 198 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 164 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL A 70 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP A 165 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 72 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 238 removed outlier: 3.621A pdb=" N ILE A 361 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 363 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THR A 334 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 260 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.602A pdb=" N VAL C 192 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 173 Processing sheet with id=AA7, first strand: chain 'I' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 12 current: chain 'I' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 193 through 201 current: chain 'I' and resid 305 through 309 Processing sheet with id=AA8, first strand: chain 'I' and resid 26 through 27 removed outlier: 3.728A pdb=" N GLU I 188 " --> pdb=" O ILE I 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 32 through 37 Processing sheet with id=AB1, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AB2, first strand: chain 'I' and resid 123 through 125 removed outlier: 4.600A pdb=" N ALA I 125 " --> pdb=" O ARG I 130 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG I 130 " --> pdb=" O ALA I 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 2 through 14 current: chain 'J' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 201 current: chain 'J' and resid 305 through 309 removed outlier: 6.971A pdb=" N VAL J 306 " --> pdb=" O THR J 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AB5, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AB6, first strand: chain 'J' and resid 123 through 124 Processing sheet with id=AB7, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 183 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 183 through 201 current: chain 'K' and resid 304 through 309 removed outlier: 9.027A pdb=" N THR K 320 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL K 306 " --> pdb=" O THR K 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AB9, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AC1, first strand: chain 'K' and resid 123 through 125 Processing sheet with id=AC2, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 26 through 29 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 26 through 29 current: chain 'L' and resid 186 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 186 through 201 current: chain 'L' and resid 305 through 309 removed outlier: 6.962A pdb=" N VAL L 306 " --> pdb=" O THR L 320 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL L 322 " --> pdb=" O VAL L 306 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR L 308 " --> pdb=" O VAL L 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AC4, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AC5, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC6, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 190 through 196 current: chain 'M' and resid 306 through 309 removed outlier: 6.913A pdb=" N VAL M 306 " --> pdb=" O THR M 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 26 through 27 Processing sheet with id=AC8, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AC9, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AD1, first strand: chain 'M' and resid 123 through 124 removed outlier: 3.590A pdb=" N PHE M 123 " --> pdb=" O ARG M 132 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG M 132 " --> pdb=" O PHE M 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'M' and resid 213 through 215 Processing sheet with id=AD3, first strand: chain 'N' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 12 current: chain 'N' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 193 through 201 current: chain 'N' and resid 305 through 309 removed outlier: 6.550A pdb=" N VAL N 306 " --> pdb=" O THR N 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'N' and resid 26 through 27 Processing sheet with id=AD5, first strand: chain 'N' and resid 31 through 36 Processing sheet with id=AD6, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AD7, first strand: chain 'N' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'O' and resid 136 through 138 removed outlier: 3.813A pdb=" N GLU O 265 " --> pdb=" O ARG O 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG O 10 " --> pdb=" O VAL O 263 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL O 263 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 32 through 35 removed outlier: 3.772A pdb=" N THR O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL O 47 " --> pdb=" O THR O 32 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 94 through 96 removed outlier: 3.640A pdb=" N ALA O 95 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 123 through 125 Processing sheet with id=AE3, first strand: chain 'P' and resid 77 through 80 removed outlier: 4.478A pdb=" N TRP P 157 " --> pdb=" O CYS P 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 85 through 87 removed outlier: 3.788A pdb=" N ILE P 85 " --> pdb=" O PHE P 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN P 87 " --> pdb=" O TYR P 113 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 90 through 94 Processing sheet with id=AE6, first strand: chain 'P' and resid 145 through 146 removed outlier: 4.482A pdb=" N SER P 151 " --> pdb=" O ILE P 146 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 168 through 169 Processing sheet with id=AE8, first strand: chain 'P' and resid 174 through 175 removed outlier: 3.502A pdb=" N ALA P 174 " --> pdb=" O TYR P 218 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 243 through 246 1054 hydrogen bonds defined for protein. 3042 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 12.09 Time building geometry restraints manager: 15.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10665 1.34 - 1.46: 5623 1.46 - 1.58: 17801 1.58 - 1.70: 88 1.70 - 1.82: 144 Bond restraints: 34321 Sorted by residual: bond pdb=" N ALA A 611 " pdb=" CA ALA A 611 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.24e-02 6.50e+03 4.34e+00 bond pdb=" C TYR A 450 " pdb=" N PRO A 451 " ideal model delta sigma weight residual 1.336 1.353 -0.017 9.80e-03 1.04e+04 2.90e+00 bond pdb=" CB PRO A 453 " pdb=" CG PRO A 453 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.34e+00 bond pdb=" CA GLY N 153 " pdb=" C GLY N 153 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.15e+00 bond pdb=" C LEU A 610 " pdb=" N ALA A 611 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.31e-02 5.83e+03 1.88e+00 ... (remaining 34316 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.02: 1186 107.02 - 113.77: 19345 113.77 - 120.53: 12965 120.53 - 127.28: 12834 127.28 - 134.03: 394 Bond angle restraints: 46724 Sorted by residual: angle pdb=" N GLY N 153 " pdb=" CA GLY N 153 " pdb=" C GLY N 153 " ideal model delta sigma weight residual 111.67 116.36 -4.69 9.20e-01 1.18e+00 2.60e+01 angle pdb=" N ILE A 59 " pdb=" CA ILE A 59 " pdb=" C ILE A 59 " ideal model delta sigma weight residual 111.77 107.11 4.66 1.04e+00 9.25e-01 2.01e+01 angle pdb=" C ARG A 426 " pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 121.97 129.51 -7.54 1.80e+00 3.09e-01 1.76e+01 angle pdb=" C ALA P 75 " pdb=" N VAL P 76 " pdb=" CA VAL P 76 " ideal model delta sigma weight residual 120.49 125.89 -5.40 1.38e+00 5.25e-01 1.53e+01 angle pdb=" N ALA A 587 " pdb=" CA ALA A 587 " pdb=" C ALA A 587 " ideal model delta sigma weight residual 108.23 113.39 -5.16 1.38e+00 5.25e-01 1.40e+01 ... (remaining 46719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 20269 35.66 - 71.32: 351 71.32 - 106.98: 35 106.98 - 142.64: 1 142.64 - 178.30: 5 Dihedral angle restraints: 20661 sinusoidal: 8524 harmonic: 12137 Sorted by residual: dihedral pdb=" O4' U R 3 " pdb=" C1' U R 3 " pdb=" N1 U R 3 " pdb=" C2 U R 3 " ideal model delta sinusoidal sigma weight residual 200.00 44.08 155.92 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U R 14 " pdb=" C1' U R 14 " pdb=" N1 U R 14 " pdb=" C2 U R 14 " ideal model delta sinusoidal sigma weight residual 200.00 48.59 151.41 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 108 " pdb=" CB CYS D 108 " ideal model delta sinusoidal sigma weight residual 93.00 18.32 74.68 1 1.00e+01 1.00e-02 7.06e+01 ... (remaining 20658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4477 0.053 - 0.107: 771 0.107 - 0.160: 129 0.160 - 0.213: 6 0.213 - 0.266: 2 Chirality restraints: 5385 Sorted by residual: chirality pdb=" CB ILE A 492 " pdb=" CA ILE A 492 " pdb=" CG1 ILE A 492 " pdb=" CG2 ILE A 492 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C3' A R 1 " pdb=" C4' A R 1 " pdb=" O3' A R 1 " pdb=" C2' A R 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.28 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL A 455 " pdb=" CA VAL A 455 " pdb=" CG1 VAL A 455 " pdb=" CG2 VAL A 455 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.77e-01 ... (remaining 5382 not shown) Planarity restraints: 5826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 452 " -0.064 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO A 453 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 610 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.38e+00 pdb=" C LEU A 610 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU A 610 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 611 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 337 " 0.044 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO A 338 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.037 5.00e-02 4.00e+02 ... (remaining 5823 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 406 2.61 - 3.18: 30101 3.18 - 3.75: 54124 3.75 - 4.33: 72549 4.33 - 4.90: 118829 Nonbonded interactions: 276009 Sorted by model distance: nonbonded pdb=" NE2 HIS Q 14 " pdb="NI NI Q 302 " model vdw 2.037 2.260 nonbonded pdb=" OG SER P 14 " pdb=" OD1 ASP P 148 " model vdw 2.114 2.440 nonbonded pdb=" OG SER P 52 " pdb=" O SER P 54 " model vdw 2.140 2.440 nonbonded pdb=" OG1 THR Q 10 " pdb=" OE1 GLU Q 13 " model vdw 2.166 2.440 nonbonded pdb=" O ALA A 44 " pdb=" OG1 THR A 48 " model vdw 2.168 2.440 ... (remaining 276004 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 'D' selection = (chain 'E' and resid 3 through 109) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 164 or resid 180 th \ rough 335)) selection = (chain 'J' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 164 or resid 180 through 335)) selection = (chain 'K' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'L' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'M' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'N' and resid 1 through 335) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ni 2 6.56 5 P 44 5.49 5 S 80 5.16 5 C 21341 2.51 5 N 5740 2.21 5 O 6374 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.780 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: 7.000 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.280 Process input model: 93.170 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4633 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 : 0.002 0.077 34321 Z= 0.143 Angle : 0.544 8.961 46724 Z= 0.293 Chirality : 0.041 0.266 5385 Planarity : 0.004 0.097 5826 Dihedral : 14.373 178.299 12835 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.46 % Favored : 92.16 % Rotamer Outliers : 0.03 % 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: -1.00 (0.13), residues: 4144 helix: 0.66 (0.15), residues: 1432 sheet: -0.55 (0.21), residues: 673 loop : -1.70 (0.14), residues: 2039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 887 time to evaluate : 3.980 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 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: 888 average time/residue: 0.5117 time to fit residues: 699.4996 Evaluate side-chains 440 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 4.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 0.9980 chunk 314 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 212 optimal weight: 0.6980 chunk 168 optimal weight: 8.9990 chunk 325 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 376 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN C 228 HIS E 83 GLN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN K 53 ASN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN M 57 HIS ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN Q 70 GLN ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4975 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 34321 Z= 0.267 Angle : 0.759 14.682 46724 Z= 0.383 Chirality : 0.046 0.216 5385 Planarity : 0.006 0.147 5826 Dihedral : 8.941 178.373 5085 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.33 % Favored : 91.31 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 4144 helix: 0.03 (0.14), residues: 1443 sheet: -0.48 (0.21), residues: 636 loop : -1.78 (0.13), residues: 2065 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 518 time to evaluate : 3.870 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 outliers start: 99 outliers final: 49 residues processed: 586 average time/residue: 0.4810 time to fit residues: 444.6124 Evaluate side-chains 430 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 381 time to evaluate : 4.003 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3509 time to fit residues: 35.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 313 optimal weight: 7.9990 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 377 optimal weight: 0.0570 chunk 407 optimal weight: 0.9990 chunk 336 optimal weight: 3.9990 chunk 374 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 209 HIS G 86 ASN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 310 ASN ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 296 ASN N 19 GLN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.097 34321 Z= 0.400 Angle : 0.917 22.637 46724 Z= 0.466 Chirality : 0.052 0.321 5385 Planarity : 0.007 0.153 5826 Dihedral : 9.379 179.678 5085 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.03 % Favored : 90.66 % Rotamer Outliers : 3.47 % 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 (0.13), residues: 4144 helix: -0.49 (0.13), residues: 1437 sheet: -0.93 (0.21), residues: 634 loop : -2.06 (0.13), residues: 2073 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 491 time to evaluate : 3.952 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 outliers start: 119 outliers final: 51 residues processed: 580 average time/residue: 0.4502 time to fit residues: 427.0255 Evaluate side-chains 425 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 374 time to evaluate : 3.948 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.3639 time to fit residues: 38.3654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 0.8980 chunk 401 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 359 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS C 165 HIS I 19 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.7262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 34321 Z= 0.248 Angle : 0.723 20.756 46724 Z= 0.362 Chirality : 0.046 0.325 5385 Planarity : 0.005 0.100 5826 Dihedral : 9.107 170.600 5085 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.11 % Favored : 91.55 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 4144 helix: -0.23 (0.14), residues: 1437 sheet: -0.86 (0.21), residues: 614 loop : -2.04 (0.13), residues: 2093 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 435 time to evaluate : 3.921 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: 60 outliers final: 28 residues processed: 479 average time/residue: 0.4684 time to fit residues: 370.7087 Evaluate side-chains 406 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 378 time to evaluate : 4.428 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3414 time to fit residues: 23.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 298 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 342 optimal weight: 0.9990 chunk 277 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 360 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 HIS K 59 HIS ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 34321 Z= 0.200 Angle : 0.675 14.772 46724 Z= 0.334 Chirality : 0.045 0.248 5385 Planarity : 0.005 0.101 5826 Dihedral : 8.987 176.440 5085 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.20 % Favored : 91.48 % Rotamer Outliers : 1.57 % 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: -1.72 (0.13), residues: 4144 helix: -0.06 (0.14), residues: 1460 sheet: -0.87 (0.21), residues: 603 loop : -2.06 (0.13), residues: 2081 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 417 time to evaluate : 4.448 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: 54 outliers final: 26 residues processed: 455 average time/residue: 0.4395 time to fit residues: 328.9629 Evaluate side-chains 399 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 373 time to evaluate : 4.305 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2986 time to fit residues: 20.2262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 7.9990 chunk 361 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 333 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 223 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 1.0024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 34321 Z= 0.367 Angle : 0.870 19.325 46724 Z= 0.449 Chirality : 0.052 0.392 5385 Planarity : 0.007 0.100 5826 Dihedral : 9.280 178.301 5085 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 30.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.21 % Favored : 89.45 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.03 % 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: -2.19 (0.13), residues: 4144 helix: -0.51 (0.13), residues: 1438 sheet: -0.89 (0.22), residues: 559 loop : -2.33 (0.13), residues: 2147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 432 time to evaluate : 3.982 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 outliers start: 113 outliers final: 47 residues processed: 509 average time/residue: 0.4548 time to fit residues: 381.2916 Evaluate side-chains 397 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 350 time to evaluate : 4.157 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3333 time to fit residues: 33.7532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 228 optimal weight: 0.0030 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 338 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 399 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 243 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 1.0396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 34321 Z= 0.227 Angle : 0.741 15.107 46724 Z= 0.368 Chirality : 0.047 0.242 5385 Planarity : 0.005 0.100 5826 Dihedral : 9.057 179.514 5085 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.23 % Favored : 91.39 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 4144 helix: -0.25 (0.14), residues: 1456 sheet: -0.79 (0.22), residues: 564 loop : -2.26 (0.13), residues: 2124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 398 time to evaluate : 4.078 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: 50 outliers final: 19 residues processed: 433 average time/residue: 0.4714 time to fit residues: 341.6332 Evaluate side-chains 357 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 338 time to evaluate : 4.028 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3417 time to fit residues: 17.6513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 197 optimal weight: 0.0270 chunk 37 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN K 17 ASN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 1.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 34321 Z= 0.222 Angle : 0.737 14.752 46724 Z= 0.363 Chirality : 0.047 0.378 5385 Planarity : 0.005 0.100 5826 Dihedral : 8.954 179.696 5085 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.42 % Favored : 91.22 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 4144 helix: -0.21 (0.14), residues: 1467 sheet: -0.83 (0.21), residues: 578 loop : -2.22 (0.13), residues: 2099 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 373 time to evaluate : 4.231 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: 28 outliers final: 9 residues processed: 396 average time/residue: 0.4587 time to fit residues: 300.9625 Evaluate side-chains 351 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 342 time to evaluate : 3.936 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4440 time to fit residues: 13.2013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 372 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 336 optimal weight: 0.8980 chunk 352 optimal weight: 2.9990 chunk 371 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 1.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 34321 Z= 0.226 Angle : 0.749 16.768 46724 Z= 0.367 Chirality : 0.046 0.300 5385 Planarity : 0.005 0.100 5826 Dihedral : 8.903 179.839 5085 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.37 % Favored : 91.26 % Rotamer Outliers : 1.02 % 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: -1.89 (0.13), residues: 4144 helix: -0.19 (0.14), residues: 1467 sheet: -0.81 (0.21), residues: 601 loop : -2.23 (0.13), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 365 time to evaluate : 4.491 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: 35 outliers final: 13 residues processed: 390 average time/residue: 0.4451 time to fit residues: 288.9983 Evaluate side-chains 348 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 335 time to evaluate : 4.111 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3415 time to fit residues: 13.6875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 2.9990 chunk 394 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 413 optimal weight: 7.9990 chunk 380 optimal weight: 1.9990 chunk 329 optimal weight: 0.0170 chunk 34 optimal weight: 0.7980 chunk 254 optimal weight: 0.7980 chunk 201 optimal weight: 0.4980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 HIS O 53 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 moved from start: 1.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 34321 Z= 0.198 Angle : 0.748 14.807 46724 Z= 0.363 Chirality : 0.046 0.382 5385 Planarity : 0.005 0.101 5826 Dihedral : 8.862 179.463 5085 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.92 % Favored : 91.72 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 4144 helix: -0.16 (0.14), residues: 1476 sheet: -0.76 (0.22), residues: 587 loop : -2.19 (0.13), residues: 2081 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 348 time to evaluate : 4.149 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: 11 outliers final: 6 residues processed: 355 average time/residue: 0.4352 time to fit residues: 258.8985 Evaluate side-chains 322 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 316 time to evaluate : 3.867 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3631 time to fit residues: 9.0844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 0.5980 chunk 350 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 303 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 329 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 ASN N 162 HIS O 53 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.110413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.089672 restraints weight = 149662.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.092378 restraints weight = 87350.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.094129 restraints weight = 58701.900| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 1.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 34321 Z= 0.199 Angle : 0.743 13.983 46724 Z= 0.360 Chirality : 0.046 0.336 5385 Planarity : 0.005 0.101 5826 Dihedral : 8.809 179.255 5085 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.33 % Favored : 91.34 % Rotamer Outliers : 0.20 % 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: -1.77 (0.13), residues: 4144 helix: -0.12 (0.14), residues: 1454 sheet: -0.74 (0.22), residues: 582 loop : -2.12 (0.13), residues: 2108 =============================================================================== Job complete usr+sys time: 7416.18 seconds wall clock time: 135 minutes 9.65 seconds (8109.65 seconds total)