Starting phenix.real_space_refine on Tue Dec 12 14:33:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1g_11985/12_2023/7b1g_11985_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 14134 2.51 5 N 3555 2.21 5 O 3856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 94": "OD1" <-> "OD2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 707": "OE1" <-> "OE2" Residue "B ARG 715": "NH1" <-> "NH2" Residue "B TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "B ASP 723": "OD1" <-> "OD2" Residue "B GLU 727": "OE1" <-> "OE2" Residue "B GLU 732": "OE1" <-> "OE2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C ARG 296": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C ASP 466": "OD1" <-> "OD2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "C PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C GLU 707": "OE1" <-> "OE2" Residue "C ARG 715": "NH1" <-> "NH2" Residue "C ARG 722": "NH1" <-> "NH2" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C GLU 728": "OE1" <-> "OE2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C ARG 746": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D ARG 296": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 394": "NH1" <-> "NH2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D ASP 438": "OD1" <-> "OD2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 707": "OE1" <-> "OE2" Residue "D ARG 715": "NH1" <-> "NH2" Residue "D GLU 732": "OE1" <-> "OE2" Residue "D ARG 746": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21661 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5497 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 24, 'TRANS': 666} Chain breaks: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 47} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5226 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5226 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5220 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 22, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {' CA': 1, '44E': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.03, per 1000 atoms: 0.51 Number of scatterers: 21661 At special positions: 0 Unit cell: (144.5, 130.05, 133.45, 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) Ca 4 19.99 S 108 16.00 P 4 15.00 O 3856 8.00 N 3555 7.00 C 14134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.00 Conformation dependent library (CDL) restraints added in 4.3 seconds 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 0 sheets defined 63.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.823A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.817A pdb=" N MET A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.629A pdb=" N LEU A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 238 through 258 removed outlier: 3.676A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 removed outlier: 3.524A pdb=" N LEU A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 328 through 349 removed outlier: 3.653A pdb=" N THR A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.834A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.903A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 424 Proline residue: A 408 - end of helix removed outlier: 3.615A pdb=" N ASP A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 457 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 473 through 497 removed outlier: 4.027A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 539 removed outlier: 3.551A pdb=" N LEU A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 576 removed outlier: 4.171A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.937A pdb=" N ASN A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 647 removed outlier: 3.611A pdb=" N SER A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 695 through 721 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'E' and resid 109 through 112 No H-bonds generated for 'chain 'E' and resid 109 through 112' Processing helix chain 'E' and resid 119 through 125 removed outlier: 5.372A pdb=" N GLU E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 42 removed outlier: 3.665A pdb=" N TYR B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.556A pdb=" N LYS B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.987A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 removed outlier: 4.114A pdb=" N LEU B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.729A pdb=" N GLU B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 155 through 163 removed outlier: 4.158A pdb=" N MET B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.740A pdb=" N LEU B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.596A pdb=" N SER B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 258 removed outlier: 4.079A pdb=" N LEU B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.533A pdb=" N LEU B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 304 through 314 removed outlier: 3.929A pdb=" N GLN B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 removed outlier: 4.257A pdb=" N THR B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.649A pdb=" N CYS B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 384 removed outlier: 3.843A pdb=" N PHE B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 removed outlier: 3.798A pdb=" N LEU B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Proline residue: B 408 - end of helix removed outlier: 3.667A pdb=" N LYS B 419 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 456 removed outlier: 3.977A pdb=" N MET B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 445 " --> pdb=" O MET B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 473 through 497 removed outlier: 3.630A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 removed outlier: 3.859A pdb=" N LEU B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 538 removed outlier: 3.860A pdb=" N LEU B 528 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 536 " --> pdb=" O ASN B 532 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.677A pdb=" N GLN B 569 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 607 removed outlier: 3.523A pdb=" N ASN B 605 " --> pdb=" O PHE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.656A pdb=" N ILE B 617 " --> pdb=" O LEU B 613 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.703A pdb=" N SER B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 658 No H-bonds generated for 'chain 'B' and resid 655 through 658' Processing helix chain 'B' and resid 697 through 721 removed outlier: 3.507A pdb=" N GLU B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 708 " --> pdb=" O GLN B 704 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 718 " --> pdb=" O LYS B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.571A pdb=" N LEU B 738 " --> pdb=" O ASN B 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 42 removed outlier: 3.871A pdb=" N TYR C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.767A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.890A pdb=" N LEU C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 109 through 116 removed outlier: 3.824A pdb=" N GLU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 155 through 164 removed outlier: 3.591A pdb=" N GLN C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 removed outlier: 3.572A pdb=" N ARG C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.529A pdb=" N LEU C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 3.624A pdb=" N SER C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 258 removed outlier: 4.171A pdb=" N LEU C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS C 250 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 269 removed outlier: 3.865A pdb=" N ILE C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 292 No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 298 through 301 No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 304 through 314 Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.834A pdb=" N THR C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 333 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 349 removed outlier: 4.198A pdb=" N TYR C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 359 No H-bonds generated for 'chain 'C' and resid 356 through 359' Processing helix chain 'C' and resid 362 through 383 Processing helix chain 'C' and resid 401 through 422 Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 435 through 456 removed outlier: 3.825A pdb=" N VAL C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 445 " --> pdb=" O MET C 441 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'C' and resid 473 through 497 removed outlier: 4.026A pdb=" N ARG C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE C 493 " --> pdb=" O SER C 489 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 514 through 540 removed outlier: 4.512A pdb=" N PHE C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 528 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 576 removed outlier: 3.711A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 608 Processing helix chain 'C' and resid 612 through 627 removed outlier: 3.907A pdb=" N ASN C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 removed outlier: 3.990A pdb=" N SER C 645 " --> pdb=" O LYS C 641 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 657 No H-bonds generated for 'chain 'C' and resid 655 through 657' Processing helix chain 'C' and resid 699 through 717 removed outlier: 3.945A pdb=" N GLU C 707 " --> pdb=" O HIS C 703 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 708 " --> pdb=" O GLN C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 749 removed outlier: 3.724A pdb=" N PHE C 745 " --> pdb=" O ASP C 741 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU C 748 " --> pdb=" O SER C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.832A pdb=" N TYR D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 removed outlier: 3.599A pdb=" N LYS D 49 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 79 removed outlier: 3.803A pdb=" N ALA D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 removed outlier: 3.894A pdb=" N LEU D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 4.591A pdb=" N LEU D 100 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 116 removed outlier: 4.430A pdb=" N GLU D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 152 Processing helix chain 'D' and resid 155 through 164 removed outlier: 4.270A pdb=" N LYS D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.849A pdb=" N ILE D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 216 through 234 removed outlier: 3.883A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 258 removed outlier: 3.833A pdb=" N LEU D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.705A pdb=" N ILE D 268 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 308 through 314 Processing helix chain 'D' and resid 326 through 349 removed outlier: 4.667A pdb=" N MET D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Proline residue: D 341 - end of helix removed outlier: 4.463A pdb=" N TYR D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 362 through 383 removed outlier: 4.015A pdb=" N PHE D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 382 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 424 removed outlier: 3.780A pdb=" N LEU D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Proline residue: D 408 - end of helix removed outlier: 3.955A pdb=" N ASP D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 456 removed outlier: 3.802A pdb=" N MET D 437 " --> pdb=" O TRP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 473 through 489 Processing helix chain 'D' and resid 492 through 497 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 514 through 517 No H-bonds generated for 'chain 'D' and resid 514 through 517' Processing helix chain 'D' and resid 522 through 532 removed outlier: 3.804A pdb=" N LEU D 528 " --> pdb=" O CYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 538 removed outlier: 3.922A pdb=" N TYR D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 534 through 538' Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 591 through 608 Processing helix chain 'D' and resid 612 through 626 removed outlier: 3.970A pdb=" N ASN D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 647 removed outlier: 3.857A pdb=" N SER D 645 " --> pdb=" O LYS D 641 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE D 647 " --> pdb=" O TRP D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 658 No H-bonds generated for 'chain 'D' and resid 655 through 658' Processing helix chain 'D' and resid 699 through 724 removed outlier: 3.578A pdb=" N GLU D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 708 " --> pdb=" O GLN D 704 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 752 removed outlier: 3.616A pdb=" N GLU D 748 " --> pdb=" O SER D 744 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY D 751 " --> pdb=" O TYR D 747 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 8.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3438 1.31 - 1.43: 6155 1.43 - 1.56: 12404 1.56 - 1.69: 4 1.69 - 1.81: 177 Bond restraints: 22178 Sorted by residual: bond pdb=" CA LEU C 520 " pdb=" C LEU C 520 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.72e-02 3.38e+03 6.01e+00 bond pdb=" C PHE B 340 " pdb=" N PRO B 341 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.20e-02 6.94e+03 4.57e+00 bond pdb=" CG1 ILE C 552 " pdb=" CD1 ILE C 552 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CA GLN A 258 " pdb=" C GLN A 258 " ideal model delta sigma weight residual 1.523 1.495 0.029 1.80e-02 3.09e+03 2.53e+00 bond pdb=" C ASP A 67 " pdb=" N PRO A 68 " ideal model delta sigma weight residual 1.337 1.351 -0.015 9.80e-03 1.04e+04 2.29e+00 ... (remaining 22173 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.09: 401 106.09 - 113.09: 12129 113.09 - 120.10: 8389 120.10 - 127.10: 8888 127.10 - 134.11: 282 Bond angle restraints: 30089 Sorted by residual: angle pdb=" N ARG B 322 " pdb=" CA ARG B 322 " pdb=" C ARG B 322 " ideal model delta sigma weight residual 114.04 108.85 5.19 1.24e+00 6.50e-01 1.75e+01 angle pdb=" CB MET A 339 " pdb=" CG MET A 339 " pdb=" SD MET A 339 " ideal model delta sigma weight residual 112.70 122.55 -9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C ASN C 558 " pdb=" N ASN C 559 " pdb=" CA ASN C 559 " ideal model delta sigma weight residual 121.54 126.80 -5.26 1.91e+00 2.74e-01 7.58e+00 angle pdb=" N PRO A 655 " pdb=" CA PRO A 655 " pdb=" C PRO A 655 " ideal model delta sigma weight residual 110.70 113.98 -3.28 1.22e+00 6.72e-01 7.21e+00 angle pdb=" CA LEU A 203 " pdb=" CB LEU A 203 " pdb=" CG LEU A 203 " ideal model delta sigma weight residual 116.30 125.60 -9.30 3.50e+00 8.16e-02 7.07e+00 ... (remaining 30084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 12078 23.98 - 47.95: 903 47.95 - 71.93: 79 71.93 - 95.90: 25 95.90 - 119.88: 4 Dihedral angle restraints: 13089 sinusoidal: 5155 harmonic: 7934 Sorted by residual: dihedral pdb=" CA MET D 470 " pdb=" C MET D 470 " pdb=" N TRP D 471 " pdb=" CA TRP D 471 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU D 374 " pdb=" C LEU D 374 " pdb=" N THR D 375 " pdb=" CA THR D 375 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA TYR A 582 " pdb=" C TYR A 582 " pdb=" N VAL A 583 " pdb=" CA VAL A 583 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 13086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1940 0.036 - 0.071: 1103 0.071 - 0.107: 285 0.107 - 0.143: 67 0.143 - 0.178: 7 Chirality restraints: 3402 Sorted by residual: chirality pdb=" CA ASN C 559 " pdb=" N ASN C 559 " pdb=" C ASN C 559 " pdb=" CB ASN C 559 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ARG A 553 " pdb=" N ARG A 553 " pdb=" C ARG A 553 " pdb=" CB ARG A 553 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA PHE C 340 " pdb=" N PHE C 340 " pdb=" C PHE C 340 " pdb=" CB PHE C 340 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 3399 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 433 " -0.016 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP D 433 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 433 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 433 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 433 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 433 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 433 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 433 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 433 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 205 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 206 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 303 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 304 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " 0.028 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3767 2.75 - 3.29: 22909 3.29 - 3.83: 34835 3.83 - 4.36: 43024 4.36 - 4.90: 70585 Nonbonded interactions: 175120 Sorted by model distance: nonbonded pdb=" OD1 ASN D 153 " pdb=" OG SER D 207 " model vdw 2.213 2.440 nonbonded pdb=" NH1 ARG A 272 " pdb=" OD1 ASP A 274 " model vdw 2.215 2.520 nonbonded pdb=" O LEU B 571 " pdb=" OH TYR B 604 " model vdw 2.216 2.440 nonbonded pdb=" O ARG E 107 " pdb=" OG1 THR E 111 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR C 523 " pdb=" OH TYR C 604 " model vdw 2.220 2.440 ... (remaining 175115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 272 or resid 284 through 660 or resid 696 throu \ gh 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 753)) selection = (chain 'B' and (resid 28 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 461 or (resid 462 and (name N o \ r name CA or name C or name O or name CB )) or resid 463 through 721 or (resid 7 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 723 through \ 753)) selection = (chain 'C' and (resid 28 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 461 or (resid 462 and (name N o \ r name CA or name C or name O or name CB )) or resid 463 through 721 or (resid 7 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 723 through \ 753)) selection = (chain 'D' and (resid 28 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 461 or (resid 462 and (name N o \ r name CA or name C or name O or name CB )) or resid 463 through 753)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 6.290 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 55.990 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.006 0.066 22178 Z= 0.406 Angle : 0.724 9.847 30089 Z= 0.374 Chirality : 0.045 0.178 3402 Planarity : 0.005 0.051 3748 Dihedral : 15.843 119.877 7927 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.09 % Allowed : 1.04 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2643 helix: -1.15 (0.12), residues: 1792 sheet: None (None), residues: 0 loop : -1.88 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 433 HIS 0.008 0.001 HIS B 102 PHE 0.023 0.002 PHE B 300 TYR 0.030 0.002 TYR D 200 ARG 0.010 0.001 ARG B 722 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 2.538 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 280 average time/residue: 0.3209 time to fit residues: 143.4774 Evaluate side-chains 225 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 308 GLN C 605 ASN C 614 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 614 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22178 Z= 0.227 Angle : 0.630 9.562 30089 Z= 0.316 Chirality : 0.042 0.208 3402 Planarity : 0.005 0.046 3748 Dihedral : 6.973 119.186 2929 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.87 % Allowed : 10.05 % Favored : 89.08 % 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: -1.38 (0.16), residues: 2643 helix: -0.43 (0.12), residues: 1851 sheet: None (None), residues: 0 loop : -1.85 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 326 HIS 0.005 0.001 HIS C 151 PHE 0.020 0.002 PHE A 271 TYR 0.029 0.001 TYR A 429 ARG 0.005 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 264 time to evaluate : 2.640 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 276 average time/residue: 0.3282 time to fit residues: 143.4054 Evaluate side-chains 247 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 233 time to evaluate : 2.562 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1977 time to fit residues: 8.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 83 optimal weight: 0.0670 chunk 195 optimal weight: 4.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22178 Z= 0.262 Angle : 0.588 8.097 30089 Z= 0.297 Chirality : 0.042 0.211 3402 Planarity : 0.004 0.041 3748 Dihedral : 6.672 119.364 2929 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.13 % Allowed : 13.75 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2643 helix: -0.12 (0.12), residues: 1843 sheet: None (None), residues: 0 loop : -1.80 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 326 HIS 0.007 0.001 HIS C 626 PHE 0.018 0.002 PHE B 300 TYR 0.029 0.001 TYR A 429 ARG 0.005 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 256 time to evaluate : 2.887 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 273 average time/residue: 0.3278 time to fit residues: 141.9003 Evaluate side-chains 240 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 225 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1979 time to fit residues: 9.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 259 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 231 optimal weight: 0.3980 chunk 69 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS B 303 GLN B 307 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22178 Z= 0.157 Angle : 0.541 11.049 30089 Z= 0.271 Chirality : 0.039 0.213 3402 Planarity : 0.004 0.040 3748 Dihedral : 6.318 116.687 2929 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.22 % Allowed : 16.71 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2643 helix: 0.23 (0.12), residues: 1847 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 326 HIS 0.012 0.001 HIS C 626 PHE 0.017 0.001 PHE A 271 TYR 0.021 0.001 TYR B 445 ARG 0.006 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 270 time to evaluate : 2.533 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 288 average time/residue: 0.3293 time to fit residues: 150.1833 Evaluate side-chains 243 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 2.518 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2521 time to fit residues: 7.6880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 106 optimal weight: 0.0670 chunk 221 optimal weight: 0.9990 chunk 179 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 232 optimal weight: 0.0770 chunk 65 optimal weight: 5.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN B 625 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22178 Z= 0.138 Angle : 0.534 10.290 30089 Z= 0.265 Chirality : 0.039 0.194 3402 Planarity : 0.004 0.046 3748 Dihedral : 6.009 112.009 2929 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.26 % Allowed : 17.62 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2643 helix: 0.49 (0.13), residues: 1839 sheet: None (None), residues: 0 loop : -1.56 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 326 HIS 0.007 0.001 HIS C 626 PHE 0.021 0.001 PHE C 439 TYR 0.023 0.001 TYR B 445 ARG 0.006 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 279 time to evaluate : 2.669 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 302 average time/residue: 0.3429 time to fit residues: 162.8639 Evaluate side-chains 245 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 233 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2626 time to fit residues: 10.0143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 136 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN A 704 GLN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22178 Z= 0.230 Angle : 0.569 9.776 30089 Z= 0.279 Chirality : 0.041 0.300 3402 Planarity : 0.004 0.043 3748 Dihedral : 6.049 109.247 2929 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.09 % Allowed : 19.28 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2643 helix: 0.53 (0.12), residues: 1845 sheet: None (None), residues: 0 loop : -1.57 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 326 HIS 0.004 0.001 HIS C 626 PHE 0.030 0.001 PHE B 300 TYR 0.018 0.001 TYR B 445 ARG 0.004 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 249 time to evaluate : 2.530 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 263 average time/residue: 0.3266 time to fit residues: 136.4729 Evaluate side-chains 252 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 2.493 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2196 time to fit residues: 9.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN C 621 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22178 Z= 0.237 Angle : 0.576 10.272 30089 Z= 0.283 Chirality : 0.041 0.271 3402 Planarity : 0.004 0.042 3748 Dihedral : 6.135 109.562 2929 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.13 % Allowed : 19.41 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2643 helix: 0.56 (0.12), residues: 1845 sheet: None (None), residues: 0 loop : -1.56 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 314 HIS 0.004 0.001 HIS C 151 PHE 0.032 0.001 PHE A 539 TYR 0.014 0.001 TYR D 582 ARG 0.007 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 2.594 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 268 average time/residue: 0.3397 time to fit residues: 144.0545 Evaluate side-chains 242 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 232 time to evaluate : 2.570 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2018 time to fit residues: 7.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 77 optimal weight: 0.0070 chunk 50 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22178 Z= 0.208 Angle : 0.570 11.550 30089 Z= 0.280 Chirality : 0.041 0.197 3402 Planarity : 0.004 0.045 3748 Dihedral : 6.097 108.407 2929 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.96 % Allowed : 20.41 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2643 helix: 0.63 (0.12), residues: 1854 sheet: None (None), residues: 0 loop : -1.50 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 314 HIS 0.010 0.001 HIS C 626 PHE 0.025 0.001 PHE A 539 TYR 0.017 0.001 TYR B 445 ARG 0.006 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 2.774 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 257 average time/residue: 0.3368 time to fit residues: 137.7683 Evaluate side-chains 241 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 234 time to evaluate : 2.672 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2119 time to fit residues: 6.3429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 189 optimal weight: 0.1980 chunk 73 optimal weight: 10.0000 chunk 217 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22178 Z= 0.177 Angle : 0.564 11.187 30089 Z= 0.276 Chirality : 0.040 0.226 3402 Planarity : 0.004 0.042 3748 Dihedral : 5.983 105.986 2929 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.52 % Allowed : 21.19 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2643 helix: 0.73 (0.13), residues: 1857 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 314 HIS 0.007 0.001 HIS C 626 PHE 0.023 0.001 PHE C 439 TYR 0.018 0.001 TYR B 445 ARG 0.007 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 2.501 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 257 average time/residue: 0.3385 time to fit residues: 137.8648 Evaluate side-chains 236 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 2.757 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2135 time to fit residues: 5.3540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22178 Z= 0.257 Angle : 0.600 11.624 30089 Z= 0.297 Chirality : 0.042 0.199 3402 Planarity : 0.004 0.041 3748 Dihedral : 6.110 106.848 2929 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.52 % Allowed : 21.45 % Favored : 78.02 % 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: 0.05 (0.17), residues: 2643 helix: 0.71 (0.12), residues: 1851 sheet: None (None), residues: 0 loop : -1.51 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 314 HIS 0.005 0.001 HIS C 626 PHE 0.021 0.001 PHE B 300 TYR 0.016 0.001 TYR A 538 ARG 0.007 0.000 ARG B 511 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 234 time to evaluate : 2.733 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 240 average time/residue: 0.3316 time to fit residues: 127.3870 Evaluate side-chains 233 residues out of total 2397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 227 time to evaluate : 2.533 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2096 time to fit residues: 5.7593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.858 > 50: distance: 29 - 47: 28.742 distance: 34 - 56: 12.964 distance: 39 - 64: 23.484 distance: 42 - 47: 26.069 distance: 43 - 71: 24.595 distance: 47 - 48: 8.320 distance: 48 - 49: 5.329 distance: 48 - 51: 29.069 distance: 49 - 50: 13.404 distance: 49 - 56: 16.602 distance: 50 - 76: 21.668 distance: 51 - 52: 39.553 distance: 52 - 53: 17.660 distance: 53 - 54: 31.006 distance: 54 - 55: 23.767 distance: 56 - 57: 9.705 distance: 57 - 58: 6.753 distance: 57 - 60: 16.940 distance: 58 - 59: 21.308 distance: 58 - 64: 17.556 distance: 59 - 88: 32.113 distance: 60 - 61: 22.898 distance: 60 - 62: 35.786 distance: 61 - 63: 24.431 distance: 64 - 65: 25.980 distance: 65 - 66: 22.362 distance: 65 - 68: 8.106 distance: 66 - 67: 18.402 distance: 66 - 71: 26.690 distance: 68 - 69: 35.053 distance: 68 - 70: 27.342 distance: 71 - 72: 33.934 distance: 72 - 73: 6.080 distance: 72 - 75: 28.877 distance: 73 - 74: 14.453 distance: 73 - 76: 23.536 distance: 76 - 77: 9.904 distance: 77 - 78: 10.014 distance: 77 - 80: 13.933 distance: 78 - 79: 12.451 distance: 78 - 88: 10.043 distance: 80 - 81: 13.424 distance: 81 - 82: 14.580 distance: 81 - 83: 17.323 distance: 82 - 84: 4.191 distance: 83 - 85: 3.281 distance: 84 - 86: 15.641 distance: 85 - 86: 15.004 distance: 86 - 87: 13.336 distance: 88 - 89: 11.274 distance: 89 - 90: 29.773 distance: 89 - 92: 19.403 distance: 90 - 91: 9.835 distance: 90 - 95: 35.666 distance: 92 - 93: 7.264 distance: 92 - 94: 33.477 distance: 95 - 96: 17.128 distance: 96 - 97: 52.019 distance: 96 - 99: 6.575 distance: 97 - 98: 20.267 distance: 97 - 100: 39.936 distance: 100 - 101: 10.429 distance: 101 - 102: 8.181 distance: 101 - 104: 26.296 distance: 102 - 103: 21.126 distance: 102 - 105: 26.265 distance: 105 - 106: 17.447 distance: 106 - 107: 15.591 distance: 106 - 109: 23.976 distance: 107 - 108: 20.270 distance: 107 - 111: 28.751 distance: 109 - 110: 37.170 distance: 111 - 112: 43.865 distance: 112 - 113: 16.416 distance: 113 - 114: 11.380 distance: 113 - 115: 23.714