Starting phenix.real_space_refine on Mon Mar 18 19:25:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjv_9513/03_2024/5gjv_9513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjv_9513/03_2024/5gjv_9513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjv_9513/03_2024/5gjv_9513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjv_9513/03_2024/5gjv_9513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjv_9513/03_2024/5gjv_9513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjv_9513/03_2024/5gjv_9513_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= 0.007 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 3 9.91 5 P 7 5.49 5 S 123 5.16 5 C 14251 2.51 5 N 3550 2.21 5 O 3970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "A ARG 823": "NH1" <-> "NH2" Residue "A ARG 828": "NH1" <-> "NH2" Residue "A ARG 903": "NH1" <-> "NH2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A ARG 1038": "NH1" <-> "NH2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1249": "NH1" <-> "NH2" Residue "A ARG 1249": "NH1" <-> "NH2" Residue "A ARG 1302": "NH1" <-> "NH2" Residue "A ARG 1318": "NH1" <-> "NH2" Residue "A GLU 1323": "OE1" <-> "OE2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A ARG 1416": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1428": "NH1" <-> "NH2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A ARG 1447": "NH1" <-> "NH2" Residue "A ARG 1472": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "F PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 649": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21904 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10183 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1276, 10141 Classifications: {'peptide': 1276} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1235} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 1276, 10141 Classifications: {'peptide': 1276} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1235} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 10343 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 710 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 91} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1304 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 4 Chain: "F" Number of atoms: 7567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 942, 7556 Unusual residues: {'ETA': 1} Classifications: {'peptide': 941, 'undetermined': 1} Link IDs: {'CIS': 1, 'LINK_CpN': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 899} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 942, 7556 Unusual residues: {'ETA': 1} Classifications: {'peptide': 941, 'undetermined': 1} Link IDs: {'CIS': 1, 'LINK_CpN': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 899} Chain breaks: 6 bond proxies already assigned to first conformer: 7702 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 442 Unusual residues: {' CA': 2, 'NAG': 1, 'PC1': 14} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-2': 7, 'PC1:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG A 794 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 794 " occ=0.50 residue: pdb=" N AARG A 910 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 910 " occ=0.50 residue: pdb=" N ALYS A 912 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 912 " occ=0.50 residue: pdb=" N AARG A1249 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1249 " occ=0.50 residue: pdb=" N AARG F 315 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 315 " occ=0.50 Time building chain proxies: 19.81, per 1000 atoms: 0.90 Number of scatterers: 21904 At special positions: 0 Unit cell: (187.44, 184.8, 157.08, 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 3 19.99 S 123 16.00 P 7 15.00 O 3970 8.00 N 3550 7.00 C 14251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.01 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=1.93 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.05 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.27 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=1.71 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.04 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " NAG-ASN " NAG A1901 " - " ASN A 257 " " NAG D 1 " - " ASN F 350 " " NAG F1203 " - " ASN F 326 " " NAG F1206 " - " ASN F 891 " " NAG F1213 " - " ASN F 94 " " NAG F1214 " - " ASN F 606 " " NAG F1219 " - " ASN F 784 " " NAG F1220 " - " ASN F1001 " " NAG F1221 " - " ASN F 988 " " NAG G 1 " - " ASN F 615 " " NAG H 1 " - " ASN F 186 " " NAG I 1 " - " ASN F 470 " " NAG J 1 " - " ASN F 898 " " NAG K 1 " - " ASN F 678 " " NAG L 1 " - " ASN F 827 " Time building additional restraints: 9.98 Conformation dependent library (CDL) restraints added in 7.5 seconds 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 16 sheets defined 49.0% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 40 through 48 removed outlier: 3.780A pdb=" N VAL A 48 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.806A pdb=" N ALA A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 removed outlier: 3.557A pdb=" N GLU A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 116 through 119 No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 121 through 138 removed outlier: 3.561A pdb=" N LEU A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 178 Proline residue: A 172 - end of helix removed outlier: 3.835A pdb=" N GLY A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.634A pdb=" N ASN A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 218 removed outlier: 3.633A pdb=" N ILE A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.599A pdb=" N VAL A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 335 removed outlier: 3.737A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.995A pdb=" N GLU A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 373 removed outlier: 3.522A pdb=" N GLN A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 373 " --> pdb=" O TRP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.840A pdb=" N LYS A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 448 removed outlier: 4.060A pdb=" N VAL A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 484 removed outlier: 3.861A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.597A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 493' Processing helix chain 'A' and resid 495 through 516 removed outlier: 3.755A pdb=" N VAL A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 4.058A pdb=" N SER A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 558 removed outlier: 3.584A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 removed outlier: 3.842A pdb=" N ILE A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.607A pdb=" N VAL A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 628 removed outlier: 3.572A pdb=" N ASN A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 628 " --> pdb=" O ILE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 640 through 650 removed outlier: 4.157A pdb=" N PHE A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 662 removed outlier: 3.680A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.582A pdb=" N ILE A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 796 " --> pdb=" O CYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 817 removed outlier: 3.593A pdb=" N PHE A 804 " --> pdb=" O TRP A 800 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 851 removed outlier: 3.615A pdb=" N ILE A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 838 " --> pdb=" O TYR A 834 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 860 removed outlier: 4.042A pdb=" N HIS A 859 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 860 " --> pdb=" O PHE A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 856 through 860' Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.601A pdb=" N ASN A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 869 " --> pdb=" O ARG A 865 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 908 removed outlier: 3.913A pdb=" N ARG A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 902 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ARG A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Proline residue: A 904 - end of helix removed outlier: 3.883A pdb=" N ALA A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 950 removed outlier: 4.557A pdb=" N VAL A 918 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 919 " --> pdb=" O HIS A 916 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 923 " --> pdb=" O CYS A 920 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 925 " --> pdb=" O PHE A 922 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 929 " --> pdb=" O ARG A 926 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN A 930 " --> pdb=" O THR A 927 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 933 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 935 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR A 936 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 938 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN A 939 " --> pdb=" O THR A 936 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 942 " --> pdb=" O GLN A 939 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 945 " --> pdb=" O PHE A 942 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 947 " --> pdb=" O CYS A 944 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 948 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 949 " --> pdb=" O GLY A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1009 removed outlier: 4.152A pdb=" N SER A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1039 through 1042 Processing helix chain 'A' and resid 1044 through 1072 removed outlier: 3.605A pdb=" N ILE A1049 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A1067 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A1072 " --> pdb=" O PHE A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1092 removed outlier: 4.079A pdb=" N VAL A1089 " --> pdb=" O GLN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.510A pdb=" N GLN A1110 " --> pdb=" O PRO A1106 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 removed outlier: 3.511A pdb=" N PHE A1125 " --> pdb=" O GLU A1121 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A1128 " --> pdb=" O MET A1124 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A1129 " --> pdb=" O PHE A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1172 removed outlier: 3.629A pdb=" N VAL A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1204 removed outlier: 3.611A pdb=" N ILE A1191 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A1199 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1233 Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 4.038A pdb=" N ARG A1242 " --> pdb=" O ARG A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1263 removed outlier: 3.534A pdb=" N THR A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1286 removed outlier: 3.602A pdb=" N LEU A1273 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A1285 " --> pdb=" O TYR A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.608A pdb=" N LEU A1316 " --> pdb=" O ALA A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1331 removed outlier: 3.638A pdb=" N LEU A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1387 removed outlier: 3.882A pdb=" N ILE A1362 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A1363 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A1367 " --> pdb=" O SER A1363 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A1371 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A1374 " --> pdb=" O PHE A1370 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A1382 " --> pdb=" O ALA A1378 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASP A1385 " --> pdb=" O MET A1381 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR A1386 " --> pdb=" O ASP A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1409 removed outlier: 3.691A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A1404 " --> pdb=" O ASP A1400 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A1405 " --> pdb=" O GLU A1401 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP A1406 " --> pdb=" O PHE A1402 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A1407 " --> pdb=" O LYS A1403 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A1408 " --> pdb=" O ALA A1404 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1427 removed outlier: 3.914A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1450 Processing helix chain 'A' and resid 1457 through 1459 No H-bonds generated for 'chain 'A' and resid 1457 through 1459' Processing helix chain 'A' and resid 1463 through 1472 Processing helix chain 'A' and resid 1482 through 1497 removed outlier: 3.553A pdb=" N GLU A1489 " --> pdb=" O GLN A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1513 Proline residue: A1511 - end of helix Processing helix chain 'B' and resid 78 through 95 removed outlier: 5.021A pdb=" N ARG B 82 " --> pdb=" O MET B 79 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA B 85 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 86 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 90 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 91 " --> pdb=" O GLN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'C' and resid 288 through 304 removed outlier: 3.514A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 344 through 358 Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 394 through 404 removed outlier: 3.563A pdb=" N ARG C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 424 removed outlier: 4.779A pdb=" N HIS C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 439 through 457 Processing helix chain 'E' and resid 2 through 5 No H-bonds generated for 'chain 'E' and resid 2 through 5' Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.711A pdb=" N VAL E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 28 " --> pdb=" O MET E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 126 removed outlier: 3.690A pdb=" N ALA E 109 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 135 through 164 Proline residue: E 139 - end of helix removed outlier: 3.654A pdb=" N PHE E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR E 144 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 146 " --> pdb=" O PHE E 143 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 149 " --> pdb=" O PHE E 146 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS E 150 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 153 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL E 157 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 159 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER E 161 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL E 162 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 164 " --> pdb=" O SER E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 203 Processing helix chain 'F' and resid 32 through 53 removed outlier: 3.507A pdb=" N THR F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.972A pdb=" N ASP F 61 " --> pdb=" O HIS F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 111 removed outlier: 3.634A pdb=" N SER F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA F 98 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU F 107 " --> pdb=" O ALA F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 201 removed outlier: 3.883A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.983A pdb=" N ILE F 274 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 326 removed outlier: 3.728A pdb=" N LEU F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN F 325 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 345 removed outlier: 3.645A pdb=" N PHE F 341 " --> pdb=" O LYS F 337 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN F 345 " --> pdb=" O PHE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 378 removed outlier: 3.829A pdb=" N ALA F 376 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 407 removed outlier: 3.792A pdb=" N ALA F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 removed outlier: 4.598A pdb=" N GLN F 426 " --> pdb=" O ARG F 422 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU F 427 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR F 428 " --> pdb=" O ASN F 424 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU F 429 " --> pdb=" O THR F 425 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP F 430 " --> pdb=" O GLN F 426 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU F 432 " --> pdb=" O TYR F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 439 removed outlier: 4.023A pdb=" N LEU F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 434 through 439' Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 563 through 566 No H-bonds generated for 'chain 'F' and resid 563 through 566' Processing helix chain 'F' and resid 573 through 580 Processing helix chain 'F' and resid 643 through 650 Processing helix chain 'F' and resid 653 through 655 No H-bonds generated for 'chain 'F' and resid 653 through 655' Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 704 through 722 removed outlier: 3.875A pdb=" N LEU F 709 " --> pdb=" O ILE F 705 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE F 714 " --> pdb=" O LEU F 710 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 717 " --> pdb=" O GLY F 713 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN F 721 " --> pdb=" O GLU F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 754 Processing helix chain 'F' and resid 767 through 772 removed outlier: 3.723A pdb=" N LEU F 771 " --> pdb=" O TYR F 767 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 767 through 772' Processing helix chain 'F' and resid 821 through 830 Processing helix chain 'F' and resid 871 through 873 No H-bonds generated for 'chain 'F' and resid 871 through 873' Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 889 removed outlier: 3.563A pdb=" N HIS F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 1046 through 1049 No H-bonds generated for 'chain 'F' and resid 1046 through 1049' Processing sheet with id= A, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= B, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= C, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.846A pdb=" N ILE B 146 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS B 139 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TRP B 144 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 277 through 280 removed outlier: 6.107A pdb=" N ILE C 385 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL C 280 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL C 387 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 432 " --> pdb=" O TYR C 388 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 309 through 314 removed outlier: 6.493A pdb=" N LEU C 363 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR C 312 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 365 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C 314 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP C 367 " --> pdb=" O VAL C 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'E' and resid 33 through 36 removed outlier: 3.536A pdb=" N TYR E 177 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.636A pdb=" N CYS E 57 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER E 81 " --> pdb=" O ILE E 56 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 152 through 154 Processing sheet with id= I, first strand: chain 'F' and resid 167 through 169 removed outlier: 3.893A pdb=" N ALA F 167 " --> pdb=" O TYR F 219 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.727A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR F 463 " --> pdb=" O THR F 449 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 293 through 296 removed outlier: 8.520A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN F 357 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU F 257 " --> pdb=" O ASN F 357 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE F 359 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU F 259 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N MET F 361 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP F 261 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE F 363 " --> pdb=" O ASP F 261 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG F 385 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU F 362 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE F 387 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR F 364 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE F 389 " --> pdb=" O THR F 364 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR F 411 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N SER F 390 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR F 413 " --> pdb=" O SER F 390 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 585 through 595 removed outlier: 3.820A pdb=" N GLY F 586 " --> pdb=" O TRP F 611 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR F 609 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 661 through 664 removed outlier: 4.314A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR F 739 " --> pdb=" O ILE F 743 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 779 " --> pdb=" O MET F 796 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 993 through 998 removed outlier: 4.510A pdb=" N LEU F1016 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP F 857 " --> pdb=" O LEU F 862 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU F 862 " --> pdb=" O ASP F 857 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 896 through 902 removed outlier: 3.581A pdb=" N GLN F1039 " --> pdb=" O GLU F 980 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 906 through 908 756 hydrogen bonds defined for protein. 2040 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: 6.80 Time building geometry restraints manager: 10.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3438 1.26 - 1.41: 5652 1.41 - 1.56: 13001 1.56 - 1.70: 90 1.70 - 1.85: 189 Bond restraints: 22370 Sorted by residual: bond pdb=" C ARG A 171 " pdb=" O ARG A 171 " ideal model delta sigma weight residual 1.244 1.480 -0.236 9.80e-03 1.04e+04 5.80e+02 bond pdb=" C TYR F 647 " pdb=" N SER F 648 " ideal model delta sigma weight residual 1.335 1.572 -0.236 1.38e-02 5.25e+03 2.94e+02 bond pdb=" C ALA F 312 " pdb=" O ALA F 312 " ideal model delta sigma weight residual 1.233 1.370 -0.137 1.29e-02 6.01e+03 1.13e+02 bond pdb=" C CYS F1062 " pdb=" O CYS F1062 " ideal model delta sigma weight residual 1.235 1.118 0.117 1.26e-02 6.30e+03 8.67e+01 bond pdb=" C CYS F1074 " pdb=" N ETA F1075 " ideal model delta sigma weight residual 1.329 1.513 -0.184 2.00e-02 2.50e+03 8.51e+01 ... (remaining 22365 not shown) Histogram of bond angle deviations from ideal: 88.55 - 99.09: 29 99.09 - 109.62: 3458 109.62 - 120.15: 17491 120.15 - 130.69: 9142 130.69 - 141.22: 118 Bond angle restraints: 30238 Sorted by residual: angle pdb=" C ASP F 518 " pdb=" CA ASP F 518 " pdb=" CB ASP F 518 " ideal model delta sigma weight residual 108.87 88.55 20.32 1.41e+00 5.03e-01 2.08e+02 angle pdb=" O SER A1248 " pdb=" C SER A1248 " pdb=" N BARG A1249 " ideal model delta sigma weight residual 122.12 136.97 -14.85 1.06e+00 8.90e-01 1.96e+02 angle pdb=" CA SER A1248 " pdb=" C SER A1248 " pdb=" N BARG A1249 " ideal model delta sigma weight residual 117.30 101.93 15.37 1.16e+00 7.43e-01 1.75e+02 angle pdb=" C GLN F 445 " pdb=" CA GLN F 445 " pdb=" CB GLN F 445 " ideal model delta sigma weight residual 110.45 129.58 -19.13 1.73e+00 3.34e-01 1.22e+02 angle pdb=" N LYS A 540 " pdb=" CA LYS A 540 " pdb=" C LYS A 540 " ideal model delta sigma weight residual 112.38 98.91 13.47 1.22e+00 6.72e-01 1.22e+02 ... (remaining 30233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.74: 13032 27.74 - 55.48: 609 55.48 - 83.22: 98 83.22 - 110.96: 15 110.96 - 138.70: 1 Dihedral angle restraints: 13755 sinusoidal: 5947 harmonic: 7808 Sorted by residual: dihedral pdb=" CA GLU F 476 " pdb=" C GLU F 476 " pdb=" N ASN F 477 " pdb=" CA ASN F 477 " ideal model delta harmonic sigma weight residual -180.00 -113.80 -66.20 0 5.00e+00 4.00e-02 1.75e+02 dihedral pdb=" CA GLY A 629 " pdb=" C GLY A 629 " pdb=" N PRO A 630 " pdb=" CA PRO A 630 " ideal model delta harmonic sigma weight residual 180.00 -114.15 -65.85 0 5.00e+00 4.00e-02 1.73e+02 dihedral pdb=" CA PRO A 266 " pdb=" C PRO A 266 " pdb=" N GLY A 267 " pdb=" CA GLY A 267 " ideal model delta harmonic sigma weight residual 180.00 -122.94 -57.06 0 5.00e+00 4.00e-02 1.30e+02 ... (remaining 13752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.221: 3380 0.221 - 0.441: 48 0.441 - 0.662: 11 0.662 - 0.883: 1 0.883 - 1.104: 2 Chirality restraints: 3442 Sorted by residual: chirality pdb=" CA TYR F 175 " pdb=" N TYR F 175 " pdb=" C TYR F 175 " pdb=" CB TYR F 175 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN F 350 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.75e+01 ... (remaining 3439 not shown) Planarity restraints: 3763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 615 " 0.211 2.00e-02 2.50e+03 2.25e-01 6.33e+02 pdb=" CG ASN F 615 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN F 615 " -0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN F 615 " -0.330 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.291 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.129 2.00e-02 2.50e+03 1.06e-01 1.42e+02 pdb=" C7 NAG G 2 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.170 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 281 " -0.035 2.00e-02 2.50e+03 7.06e-02 4.99e+01 pdb=" C GLY C 281 " 0.122 2.00e-02 2.50e+03 pdb=" O GLY C 281 " -0.046 2.00e-02 2.50e+03 pdb=" N PRO C 282 " -0.041 2.00e-02 2.50e+03 ... (remaining 3760 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.34: 51 2.34 - 2.98: 10771 2.98 - 3.62: 30644 3.62 - 4.26: 48409 4.26 - 4.90: 77924 Nonbonded interactions: 167799 Sorted by model distance: nonbonded pdb=" CE1 PHE F 515 " pdb=" CB ALA F 623 " model vdw 1.695 3.760 nonbonded pdb=" ND2 ASN F 297 " pdb=" O LYS F 330 " model vdw 1.906 2.520 nonbonded pdb=" OD1 ASP A 362 " pdb=" ND2 ASN C 437 " model vdw 1.930 2.520 nonbonded pdb=" O ASN F 528 " pdb=" ND2 ASN F 528 " model vdw 1.979 2.520 nonbonded pdb=" O SER F 671 " pdb=" OD1 ASP F 672 " model vdw 1.986 3.040 ... (remaining 167794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 4.850 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 72.180 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.236 22370 Z= 0.828 Angle : 1.615 22.467 30238 Z= 0.920 Chirality : 0.084 1.104 3442 Planarity : 0.008 0.114 3748 Dihedral : 15.743 138.701 8674 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 1.99 % Allowed : 11.57 % Favored : 86.45 % Rotamer: Outliers : 4.57 % Allowed : 4.22 % Favored : 91.21 % Cbeta Deviations : 1.27 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.04 % Twisted Proline : 3.74 % Twisted General : 0.75 % 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: -5.08 (0.13), residues: 2633 helix: -3.62 (0.09), residues: 1296 sheet: -1.54 (0.32), residues: 233 loop : -3.32 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP F 403 HIS 0.013 0.003 HIS A 223 PHE 0.049 0.004 PHE A 581 TYR 0.054 0.005 TYR F 609 ARG 0.032 0.001 ARG F 769 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 621 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable