Starting phenix.real_space_refine on Sun Sep 29 14:50:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/09_2024/7njm_12387_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/09_2024/7njm_12387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/09_2024/7njm_12387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/09_2024/7njm_12387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/09_2024/7njm_12387_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/09_2024/7njm_12387_trim.cif" } resolution = 2.84 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= 0.002 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 107 5.16 5 C 23570 2.51 5 N 6404 2.21 5 O 7181 1.98 5 H 37328 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74611 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 7659 Classifications: {'peptide': 506} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Chain breaks: 2 Chain: "B" Number of atoms: 7649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 504, 7628 Classifications: {'peptide': 504} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 504, 7628 Classifications: {'peptide': 504} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Chain breaks: 2 bond proxies already assigned to first conformer: 7662 Chain: "C" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 8004 Classifications: {'peptide': 528} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 503} Chain breaks: 2 Chain: "D" Number of atoms: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7147 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4596 Classifications: {'peptide': 299} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 288} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2161 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "d" Number of atoms: 6656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6656 Classifications: {'peptide': 438} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 354 " occ=0.40 ... (38 atoms not shown) pdb=" HZ BPHE B 354 " occ=0.40 Time building chain proxies: 30.40, per 1000 atoms: 0.41 Number of scatterers: 74611 At special positions: 0 Unit cell: (131.97, 129.48, 251.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 107 16.00 P 16 15.00 Mg 5 11.99 O 7181 8.00 N 6404 7.00 C 23570 6.00 H 37328 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.97 Conformation dependent library (CDL) restraints added in 5.8 seconds 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8878 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 28 sheets defined 61.2% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.503A pdb=" N LEU A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.940A pdb=" N ARG A 142 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 242 through 264 Proline residue: A 250 - end of helix removed outlier: 3.669A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.574A pdb=" N GLN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.665A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.567A pdb=" N LYS A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.178A pdb=" N PHE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 9 through 22 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.702A pdb=" N PHE B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.682A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.873A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 262 Proline residue: B 250 - end of helix removed outlier: 3.753A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.556A pdb=" N GLN B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.685A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 383 through 406 removed outlier: 5.156A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.696A pdb=" N LYS B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 removed outlier: 3.868A pdb=" N TYR C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.867A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.680A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 242 through 262 Proline residue: C 250 - end of helix removed outlier: 3.759A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.591A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.817A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 407 removed outlier: 5.310A pdb=" N SER C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU C 393 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.685A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 178 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 223 through 244 removed outlier: 5.046A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 4.186A pdb=" N PHE D 259 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 311 through 314 Processing helix chain 'D' and resid 317 through 324 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 362 through 390 removed outlier: 4.687A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 395 through 413 removed outlier: 3.939A pdb=" N SER D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 451 through 456 Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'E' and resid 25 through 29 removed outlier: 4.330A pdb=" N VAL E 29 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 181 removed outlier: 3.530A pdb=" N PHE E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.701A pdb=" N ARG E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 270 Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 357 through 389 removed outlier: 8.104A pdb=" N ASP E 363 " --> pdb=" O ALA E 359 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N GLU E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS E 365 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 412 Processing helix chain 'E' and resid 416 through 420 Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 451 through 455 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 91 through 95 removed outlier: 3.534A pdb=" N VAL F 94 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 95 " --> pdb=" O ASP F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 91 through 95' Processing helix chain 'F' and resid 126 through 130 Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 178 Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 223 through 246 removed outlier: 4.886A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 270 removed outlier: 3.663A pdb=" N PHE F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 282 through 294 Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 340 removed outlier: 3.570A pdb=" N LYS F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 362 through 382 Processing helix chain 'F' and resid 382 through 390 removed outlier: 3.804A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 412 Processing helix chain 'F' and resid 419 through 424 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'F' and resid 460 through 472 Processing helix chain 'G' and resid 4 through 61 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 91 through 111 Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.710A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 91 through 99 Processing helix chain 'H' and resid 103 through 118 Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.549A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 80 removed outlier: 4.071A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.008A pdb=" N ALA L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU L 72 " --> pdb=" O TYR L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.553A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 81 removed outlier: 3.661A pdb=" N PHE M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.622A pdb=" N ILE M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.941A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.337A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.657A pdb=" N ALA N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA N 76 " --> pdb=" O LEU N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.818A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 3.516A pdb=" N PHE O 54 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.636A pdb=" N ALA O 66 " --> pdb=" O GLY O 62 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR O 68 " --> pdb=" O VAL O 64 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 Processing helix chain 'P' and resid 49 through 81 removed outlier: 3.892A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.772A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.631A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.668A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 79 removed outlier: 4.758A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.579A pdb=" N ILE R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 49 through 81 removed outlier: 4.531A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.635A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 80 removed outlier: 4.058A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.722A pdb=" N ILE T 59 " --> pdb=" O THR T 55 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA T 66 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 52 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.539A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.723A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 205 Proline residue: a 182 - end of helix removed outlier: 3.799A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.601A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.972A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 48 removed outlier: 4.043A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 161 removed outlier: 3.791A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 137 Processing helix chain 'd' and resid 139 through 157 Processing helix chain 'd' and resid 173 through 192 removed outlier: 3.637A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 225 removed outlier: 4.069A pdb=" N ASN d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.610A pdb=" N ASN d 259 " --> pdb=" O THR d 255 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 287 removed outlier: 3.881A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 Processing helix chain 'd' and resid 306 through 315 Processing helix chain 'd' and resid 319 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 3.601A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 402 Processing helix chain 'd' and resid 413 through 416 Processing helix chain 'd' and resid 431 through 443 removed outlier: 3.551A pdb=" N LEU d 443 " --> pdb=" O ALA d 439 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.329A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=C, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=D, first strand: chain 'A' and resid 232 through 237 removed outlier: 6.480A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.074A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=G, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.448A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 232 through 237 removed outlier: 6.660A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.114A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=K, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.530A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'C' and resid 232 through 237 removed outlier: 8.741A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=L Processing sheet with id=M, first strand: chain 'D' and resid 10 through 16 removed outlier: 6.563A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=O, first strand: chain 'D' and resid 329 through 332 removed outlier: 7.535A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA D 188 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.513A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'E' and resid 87 through 89 Processing sheet with id=R, first strand: chain 'E' and resid 329 through 332 removed outlier: 8.591A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.496A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'F' and resid 87 through 90 removed outlier: 3.873A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'F' and resid 329 through 332 removed outlier: 7.568A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'G' and resid 196 through 204 removed outlier: 6.314A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU G 136 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.302A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'H' and resid 31 through 34 removed outlier: 4.221A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=Z, first strand: chain 'a' and resid 112 through 114 Processing sheet with id=AA, first strand: chain 'd' and resid 375 through 381 Processing sheet with id=AB, first strand: chain 'd' and resid 420 through 423 2370 hydrogen bonds defined for protein. 6843 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: 28.95 Time building geometry restraints manager: 18.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37308 1.03 - 1.23: 37 1.23 - 1.42: 15318 1.42 - 1.62: 22348 1.62 - 1.81: 194 Bond restraints: 75205 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" CG LEU L 19 " pdb=" CD1 LEU L 19 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.53e+00 bond pdb=" CG LEU T 19 " pdb=" CD2 LEU T 19 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" C ALA C 390 " pdb=" O ALA C 390 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.31e-02 5.83e+03 1.35e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 ... (remaining 75200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 132994 1.36 - 2.72: 2942 2.72 - 4.08: 260 4.08 - 5.45: 40 5.45 - 6.81: 22 Bond angle restraints: 136258 Sorted by residual: angle pdb=" N GLN b 82 " pdb=" CA GLN b 82 " pdb=" CB GLN b 82 " ideal model delta sigma weight residual 110.28 115.41 -5.13 1.55e+00 4.16e-01 1.10e+01 angle pdb=" N VAL A 519 " pdb=" CA VAL A 519 " pdb=" C VAL A 519 " ideal model delta sigma weight residual 112.29 109.37 2.92 9.40e-01 1.13e+00 9.66e+00 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.16 -5.46 1.80e+00 3.09e-01 9.19e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.06 -5.36 1.80e+00 3.09e-01 8.86e+00 angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.02 -5.32 1.80e+00 3.09e-01 8.75e+00 ... (remaining 136253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.63: 33710 32.63 - 65.26: 1369 65.26 - 97.88: 79 97.88 - 130.51: 1 130.51 - 163.14: 2 Dihedral angle restraints: 35161 sinusoidal: 19491 harmonic: 15670 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 103.14 -163.14 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 168.92 131.08 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 67.34 -127.35 1 2.00e+01 2.50e-03 3.86e+01 ... (remaining 35158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5194 0.059 - 0.118: 696 0.118 - 0.177: 59 0.177 - 0.237: 3 0.237 - 0.296: 9 Chirality restraints: 5961 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 5958 not shown) Planarity restraints: 11423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 429 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" CD GLU C 429 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU C 429 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU C 429 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 99 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C PHE a 99 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE a 99 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE a 100 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 97 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C PHE a 97 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE a 97 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL a 98 " -0.011 2.00e-02 2.50e+03 ... (remaining 11420 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1988 2.13 - 2.75: 140996 2.75 - 3.36: 228482 3.36 - 3.98: 293096 3.98 - 4.60: 462495 Nonbonded interactions: 1127057 Sorted by model distance: nonbonded pdb=" OE1 GLU d 216 " pdb=" H LEU d 219 " model vdw 1.509 2.450 nonbonded pdb=" OD1 ASN G 95 " pdb="HH21 ARG G 98 " model vdw 1.598 2.450 nonbonded pdb=" OE1 GLU E 239 " pdb="HH21 ARG E 293 " model vdw 1.600 2.450 nonbonded pdb=" O ALA a 126 " pdb=" HG SER a 129 " model vdw 1.611 2.450 nonbonded pdb=" O ARG G 76 " pdb=" H ASP G 181 " model vdw 1.612 2.450 ... (remaining 1127052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 353 or resid 356 through 406 or resid 415 throug \ h 515 or resid 518 through 519 or resid 521 or resid 600 through 601)) selection = (chain 'B' and (resid 5 through 353 or resid 356 through 406 or resid 415 throug \ h 515 or resid 518 through 519 or resid 521 or resid 600 through 601)) selection = (chain 'C' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 6 through 22 or (resid 29 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 30 through 353 or \ resid 356 through 406 or resid 415 through 515 or resid 537 through 538 or resi \ d 540 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 8 through 471) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 471)) selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 471)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = (chain 'Q' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.060 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: 1.020 Extract box with map and model: 2.100 Check model and map are aligned: 0.410 Set scattering table: 0.510 Process input model: 130.270 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.003 0.042 37877 Z= 0.183 Angle : 0.497 6.807 51371 Z= 0.264 Chirality : 0.041 0.296 5961 Planarity : 0.004 0.049 6723 Dihedral : 15.188 163.141 13871 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.41 (0.13), residues: 4879 helix: 1.72 (0.10), residues: 2637 sheet: -0.48 (0.21), residues: 577 loop : 0.34 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 118 HIS 0.002 0.001 HIS a 146 PHE 0.014 0.001 PHE B 245 TYR 0.022 0.001 TYR a 145 ARG 0.007 0.000 ARG d 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.7495 (m-30) cc_final: 0.7269 (m-30) REVERT: C 497 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7406 (tm-30) REVERT: H 119 GLN cc_start: 0.8051 (mt0) cc_final: 0.7576 (pp30) REVERT: M 32 ASP cc_start: 0.8221 (m-30) cc_final: 0.7988 (m-30) REVERT: P 77 LEU cc_start: 0.9109 (tt) cc_final: 0.8893 (tm) REVERT: Q 4 ASP cc_start: 0.7182 (t0) cc_final: 0.6859 (t0) REVERT: Q 86 GLN cc_start: 0.7724 (mm-40) cc_final: 0.6905 (pm20) REVERT: T 21 MET cc_start: 0.8168 (mmp) cc_final: 0.7952 (mmp) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 2.6392 time to fit residues: 1324.8295 Evaluate side-chains 273 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 407 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 377 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 437 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 GLN Q 71 ASN T 86 GLN a 112 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 37877 Z= 0.341 Angle : 0.558 7.021 51371 Z= 0.298 Chirality : 0.042 0.148 5961 Planarity : 0.004 0.071 6723 Dihedral : 7.307 122.819 5405 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.38 % Favored : 97.58 % Rotamer: Outliers : 0.88 % Allowed : 6.66 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.54 (0.12), residues: 4879 helix: 1.92 (0.10), residues: 2667 sheet: -0.60 (0.21), residues: 544 loop : 0.24 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 118 HIS 0.005 0.001 HIS H 38 PHE 0.019 0.001 PHE B 245 TYR 0.021 0.001 TYR a 145 ARG 0.007 0.000 ARG d 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 326 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 292 time to evaluate : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.7545 (m-30) cc_final: 0.7339 (m-30) REVERT: A 512 GLN cc_start: 0.7726 (mm110) cc_final: 0.7473 (mm-40) REVERT: C 497 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7388 (tm-30) REVERT: D 52 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: D 397 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: E 388 ILE cc_start: 0.8061 (mp) cc_final: 0.7791 (mt) REVERT: E 400 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7594 (pp30) REVERT: F 290 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8848 (tm) REVERT: G 98 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7344 (mtp85) REVERT: H 119 GLN cc_start: 0.7999 (mt0) cc_final: 0.7586 (pp30) REVERT: Q 4 ASP cc_start: 0.7224 (t0) cc_final: 0.6933 (t0) REVERT: Q 86 GLN cc_start: 0.7756 (mm-40) cc_final: 0.6905 (pm20) REVERT: b 149 ASP cc_start: 0.7763 (m-30) cc_final: 0.7532 (m-30) outliers start: 34 outliers final: 9 residues processed: 311 average time/residue: 2.4882 time to fit residues: 964.3765 Evaluate side-chains 283 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 269 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 469 GLU Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 243 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 364 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 438 optimal weight: 2.9990 chunk 473 optimal weight: 6.9990 chunk 390 optimal weight: 3.9990 chunk 434 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 chunk 351 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 GLN a 15 HIS a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37877 Z= 0.295 Angle : 0.531 6.947 51371 Z= 0.281 Chirality : 0.041 0.146 5961 Planarity : 0.004 0.070 6723 Dihedral : 7.205 120.644 5405 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Rotamer: Outliers : 0.91 % Allowed : 8.51 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.60 (0.12), residues: 4879 helix: 2.06 (0.10), residues: 2666 sheet: -0.84 (0.21), residues: 552 loop : 0.22 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.017 0.001 PHE M 74 TYR 0.020 0.001 TYR a 145 ARG 0.005 0.000 ARG D 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 329 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 294 time to evaluate : 4.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 497 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7387 (tm-30) REVERT: E 388 ILE cc_start: 0.8157 (mp) cc_final: 0.7917 (mt) REVERT: E 400 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7536 (pp30) REVERT: G 98 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7342 (mtp85) REVERT: H 119 GLN cc_start: 0.7999 (mt0) cc_final: 0.7569 (pp30) REVERT: O 75 MET cc_start: 0.8448 (tmm) cc_final: 0.8234 (tmm) REVERT: Q 4 ASP cc_start: 0.7293 (t0) cc_final: 0.6953 (t0) REVERT: Q 86 GLN cc_start: 0.7754 (mm-40) cc_final: 0.6904 (pm20) REVERT: T 63 LEU cc_start: 0.8881 (tt) cc_final: 0.8648 (tp) REVERT: b 149 ASP cc_start: 0.7772 (m-30) cc_final: 0.7528 (m-30) outliers start: 35 outliers final: 9 residues processed: 312 average time/residue: 2.4181 time to fit residues: 948.6521 Evaluate side-chains 270 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 259 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 433 optimal weight: 0.8980 chunk 329 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 294 optimal weight: 0.9980 chunk 440 optimal weight: 3.9990 chunk 465 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 417 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN E 370 GLN a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 0.062 37877 Z= 0.260 Angle : 0.520 6.805 51371 Z= 0.274 Chirality : 0.040 0.145 5961 Planarity : 0.004 0.069 6723 Dihedral : 7.053 117.878 5405 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.42 % Favored : 97.54 % Rotamer: Outliers : 0.96 % Allowed : 9.34 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.67 (0.12), residues: 4879 helix: 2.14 (0.10), residues: 2670 sheet: -0.88 (0.21), residues: 552 loop : 0.23 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE M 74 TYR 0.019 0.001 TYR a 145 ARG 0.005 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 315 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 278 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 497 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7389 (tm-30) REVERT: E 78 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: E 400 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7502 (pp30) REVERT: F 290 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8835 (tm) REVERT: G 98 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7386 (mtp85) REVERT: H 119 GLN cc_start: 0.8002 (mt0) cc_final: 0.7572 (pp30) REVERT: Q 4 ASP cc_start: 0.7289 (t0) cc_final: 0.6977 (t0) REVERT: Q 86 GLN cc_start: 0.7763 (mm-40) cc_final: 0.6905 (pm20) REVERT: b 149 ASP cc_start: 0.7753 (m-30) cc_final: 0.7512 (m-30) outliers start: 37 outliers final: 14 residues processed: 299 average time/residue: 2.5376 time to fit residues: 943.4211 Evaluate side-chains 284 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 266 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain a residue 225 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 388 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 397 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 chunk 418 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 37877 Z= 0.372 Angle : 0.551 6.924 51371 Z= 0.293 Chirality : 0.042 0.148 5961 Planarity : 0.004 0.067 6723 Dihedral : 7.184 119.340 5405 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.56 % Favored : 97.40 % Rotamer: Outliers : 1.01 % Allowed : 10.04 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.55 (0.12), residues: 4879 helix: 2.06 (0.10), residues: 2671 sheet: -0.93 (0.21), residues: 552 loop : 0.14 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS H 38 PHE 0.016 0.001 PHE E 439 TYR 0.019 0.001 TYR a 145 ARG 0.006 0.000 ARG D 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 313 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 274 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 497 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7413 (tm-30) REVERT: E 400 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7477 (pp30) REVERT: F 290 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8867 (tm) REVERT: G 98 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7369 (mtp85) REVERT: H 119 GLN cc_start: 0.8025 (mt0) cc_final: 0.7585 (pp30) REVERT: Q 4 ASP cc_start: 0.7333 (t0) cc_final: 0.6987 (t0) REVERT: Q 86 GLN cc_start: 0.7779 (mm-40) cc_final: 0.6906 (pm20) REVERT: T 75 MET cc_start: 0.7519 (tmm) cc_final: 0.7282 (tmm) REVERT: a 104 ASN cc_start: 0.8533 (m110) cc_final: 0.8238 (m110) REVERT: b 149 ASP cc_start: 0.7782 (m-30) cc_final: 0.7546 (m-30) outliers start: 39 outliers final: 18 residues processed: 299 average time/residue: 2.4795 time to fit residues: 936.5990 Evaluate side-chains 280 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain a residue 203 ILE Chi-restraints excluded: chain a residue 225 VAL Chi-restraints excluded: chain a residue 229 GLN Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 156 optimal weight: 2.9990 chunk 419 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 466 optimal weight: 0.6980 chunk 387 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN E 370 GLN G 149 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37877 Z= 0.215 Angle : 0.511 7.281 51371 Z= 0.268 Chirality : 0.040 0.154 5961 Planarity : 0.004 0.069 6723 Dihedral : 6.977 118.297 5405 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 0.75 % Allowed : 10.80 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.12), residues: 4879 helix: 2.20 (0.10), residues: 2670 sheet: -0.92 (0.21), residues: 551 loop : 0.23 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS D 121 PHE 0.016 0.001 PHE Q 74 TYR 0.019 0.001 TYR a 145 ARG 0.005 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 277 time to evaluate : 4.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 497 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7401 (tm-30) REVERT: E 78 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: E 400 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7447 (pp30) REVERT: F 290 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8789 (tm) REVERT: G 98 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7407 (mtp85) REVERT: H 119 GLN cc_start: 0.8025 (mt0) cc_final: 0.7579 (pp30) REVERT: Q 4 ASP cc_start: 0.7274 (t0) cc_final: 0.6964 (t0) REVERT: Q 65 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7585 (mp0) REVERT: Q 86 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6871 (pm20) REVERT: a 104 ASN cc_start: 0.8510 (m110) cc_final: 0.8199 (m110) REVERT: b 55 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8077 (mmtt) REVERT: b 149 ASP cc_start: 0.7776 (m-30) cc_final: 0.7560 (m-30) outliers start: 29 outliers final: 14 residues processed: 295 average time/residue: 2.4975 time to fit residues: 915.7602 Evaluate side-chains 282 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 264 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain a residue 203 ILE Chi-restraints excluded: chain a residue 225 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 449 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 392 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 464 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN E 370 GLN L 71 ASN a 192 ASN a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37877 Z= 0.227 Angle : 0.510 7.180 51371 Z= 0.267 Chirality : 0.040 0.200 5961 Planarity : 0.004 0.075 6723 Dihedral : 6.890 115.727 5405 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 0.81 % Allowed : 11.13 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.80 (0.12), residues: 4879 helix: 2.27 (0.10), residues: 2670 sheet: -0.90 (0.21), residues: 549 loop : 0.25 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS D 121 PHE 0.016 0.001 PHE P 69 TYR 0.019 0.001 TYR a 145 ARG 0.007 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 312 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 281 time to evaluate : 4.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 497 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7416 (tm-30) REVERT: E 78 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: E 400 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7385 (pp30) REVERT: F 290 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8770 (tm) REVERT: G 98 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7410 (mtp85) REVERT: H 119 GLN cc_start: 0.8032 (mt0) cc_final: 0.7584 (pp30) REVERT: Q 4 ASP cc_start: 0.7287 (t0) cc_final: 0.6971 (t0) REVERT: Q 65 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7604 (mp0) REVERT: Q 86 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6871 (pm20) REVERT: R 21 MET cc_start: 0.8447 (mmp) cc_final: 0.8110 (mmm) REVERT: a 104 ASN cc_start: 0.8534 (m110) cc_final: 0.8224 (m110) REVERT: a 192 ASN cc_start: 0.8969 (t0) cc_final: 0.8728 (t0) REVERT: b 149 ASP cc_start: 0.7795 (m-30) cc_final: 0.7565 (m-30) outliers start: 31 outliers final: 12 residues processed: 300 average time/residue: 2.5996 time to fit residues: 971.6302 Evaluate side-chains 284 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 268 time to evaluate : 4.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain a residue 203 ILE Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 287 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 277 optimal weight: 0.2980 chunk 139 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 365 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.003 0.046 37877 Z= 0.199 Angle : 0.505 7.140 51371 Z= 0.262 Chirality : 0.040 0.144 5961 Planarity : 0.004 0.078 6723 Dihedral : 6.773 113.476 5405 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.17 % Favored : 97.81 % Rotamer: Outliers : 0.73 % Allowed : 11.58 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.88 (0.12), residues: 4879 helix: 2.34 (0.10), residues: 2672 sheet: -0.90 (0.21), residues: 549 loop : 0.30 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS D 121 PHE 0.017 0.001 PHE P 69 TYR 0.020 0.001 TYR O 68 ARG 0.009 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 308 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 4.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8003 (mt-10) REVERT: C 497 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 67 MET cc_start: 0.8371 (mmt) cc_final: 0.8155 (mmt) REVERT: E 78 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: E 400 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7390 (pp30) REVERT: F 290 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8765 (tm) REVERT: G 98 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7423 (mtp85) REVERT: H 119 GLN cc_start: 0.8041 (mt0) cc_final: 0.7573 (tm-30) REVERT: Q 4 ASP cc_start: 0.7278 (t0) cc_final: 0.6985 (t0) REVERT: Q 65 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7591 (mp0) REVERT: Q 86 GLN cc_start: 0.7733 (mm-40) cc_final: 0.6868 (pm20) REVERT: a 104 ASN cc_start: 0.8523 (m110) cc_final: 0.8208 (m110) REVERT: b 149 ASP cc_start: 0.7801 (m-30) cc_final: 0.7590 (m-30) outliers start: 28 outliers final: 14 residues processed: 300 average time/residue: 2.6097 time to fit residues: 978.7329 Evaluate side-chains 289 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain a residue 225 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 422 optimal weight: 2.9990 chunk 445 optimal weight: 0.8980 chunk 406 optimal weight: 7.9990 chunk 432 optimal weight: 3.9990 chunk 444 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 409 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 37877 Z= 0.337 Angle : 0.537 7.009 51371 Z= 0.282 Chirality : 0.041 0.144 5961 Planarity : 0.004 0.081 6723 Dihedral : 6.945 115.034 5405 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.40 % Favored : 97.58 % Rotamer: Outliers : 0.68 % Allowed : 11.71 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.75 (0.12), residues: 4879 helix: 2.24 (0.10), residues: 2674 sheet: -0.93 (0.21), residues: 552 loop : 0.23 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS H 38 PHE 0.019 0.001 PHE P 69 TYR 0.020 0.001 TYR O 68 ARG 0.009 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 273 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7883 (mtp85) REVERT: C 497 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7431 (tm-30) REVERT: E 78 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: E 400 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7359 (pp30) REVERT: F 290 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8807 (tm) REVERT: G 98 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7422 (mtp85) REVERT: H 119 GLN cc_start: 0.8016 (mt0) cc_final: 0.7566 (tm-30) REVERT: Q 4 ASP cc_start: 0.7301 (t0) cc_final: 0.6982 (t0) REVERT: Q 65 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7624 (mp0) REVERT: Q 86 GLN cc_start: 0.7744 (mm-40) cc_final: 0.6826 (pm20) REVERT: a 104 ASN cc_start: 0.8539 (m110) cc_final: 0.8241 (m110) REVERT: b 149 ASP cc_start: 0.7836 (m-30) cc_final: 0.7620 (m-30) outliers start: 26 outliers final: 15 residues processed: 292 average time/residue: 2.5523 time to fit residues: 935.8034 Evaluate side-chains 288 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 269 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain a residue 225 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 431 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 457 optimal weight: 7.9990 chunk 279 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 480 optimal weight: 4.9990 chunk 441 optimal weight: 0.5980 chunk 382 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37877 Z= 0.213 Angle : 0.516 7.281 51371 Z= 0.268 Chirality : 0.040 0.145 5961 Planarity : 0.004 0.083 6723 Dihedral : 6.816 114.511 5405 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 0.52 % Allowed : 12.12 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.86 (0.12), residues: 4879 helix: 2.32 (0.10), residues: 2674 sheet: -0.93 (0.21), residues: 552 loop : 0.30 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS D 121 PHE 0.016 0.001 PHE P 69 TYR 0.021 0.001 TYR O 68 ARG 0.012 0.000 ARG D 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 279 time to evaluate : 4.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 497 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7404 (tm-30) REVERT: E 78 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: E 400 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7376 (pp30) REVERT: F 290 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8781 (tm) REVERT: G 98 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7429 (mtp85) REVERT: H 119 GLN cc_start: 0.8016 (mt0) cc_final: 0.7561 (tm-30) REVERT: Q 4 ASP cc_start: 0.7285 (t0) cc_final: 0.6993 (t0) REVERT: Q 65 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7578 (mp0) REVERT: Q 86 GLN cc_start: 0.7758 (mm-40) cc_final: 0.6842 (pm20) REVERT: a 104 ASN cc_start: 0.8532 (m110) cc_final: 0.8237 (m110) REVERT: b 55 LYS cc_start: 0.8957 (ttpt) cc_final: 0.8078 (mmtt) REVERT: b 149 ASP cc_start: 0.7813 (m-30) cc_final: 0.7608 (m-30) outliers start: 20 outliers final: 15 residues processed: 294 average time/residue: 2.5118 time to fit residues: 915.4834 Evaluate side-chains 290 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 271 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 58 PHE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain a residue 225 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain d residue 347 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 234 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 407 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 352 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 382 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 393 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.057050 restraints weight = 271002.496| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.69 r_work: 0.2848 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.340 37877 Z= 0.240 Angle : 0.641 59.265 51371 Z= 0.358 Chirality : 0.040 0.151 5961 Planarity : 0.004 0.082 6723 Dihedral : 6.818 114.507 5405 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 0.57 % Allowed : 12.07 % Favored : 87.36 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.86 (0.12), residues: 4879 helix: 2.32 (0.10), residues: 2674 sheet: -0.93 (0.21), residues: 552 loop : 0.30 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS D 121 PHE 0.090 0.001 PHE Q 58 TYR 0.019 0.001 TYR O 68 ARG 0.007 0.000 ARG D 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17754.70 seconds wall clock time: 302 minutes 6.04 seconds (18126.04 seconds total)