Starting phenix.real_space_refine on Thu Mar 21 13:15:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dar_27273/03_2024/8dar_27273_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dar_27273/03_2024/8dar_27273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dar_27273/03_2024/8dar_27273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dar_27273/03_2024/8dar_27273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dar_27273/03_2024/8dar_27273_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dar_27273/03_2024/8dar_27273_updated.pdb" } resolution = 3.0 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= -0.029 sd= 1.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 30 5.49 5 S 144 5.16 5 C 18857 2.51 5 N 5254 2.21 5 O 5870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30157 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4294 Classifications: {'peptide': 553} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 523} Chain breaks: 4 Chain: "B" Number of atoms: 4298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4298 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 525} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4248 Classifications: {'peptide': 548} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 518} Chain breaks: 3 Chain: "D" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4300 Classifications: {'peptide': 554} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 524} Chain breaks: 4 Chain: "E" Number of atoms: 4166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4166 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 508} Chain breaks: 2 Chain: "F" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4251 Classifications: {'peptide': 548} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 518} Chain breaks: 4 Chain: "G" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3815 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "H" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25810 SG CYS G 137 42.448 45.406 95.749 1.00 47.25 S ATOM 25870 SG CYS G 145 46.040 46.333 95.040 1.00 40.29 S ATOM 25897 SG CYS G 148 44.681 46.030 98.508 1.00 38.91 S ATOM 26367 SG CYS G 204 72.459 88.210 114.209 1.00 51.99 S ATOM 26465 SG CYS G 216 72.400 89.333 110.696 1.00 38.69 S ATOM 26486 SG CYS G 219 69.772 90.456 112.988 1.00 37.73 S Time building chain proxies: 15.25, per 1000 atoms: 0.51 Number of scatterers: 30157 At special positions: 0 Unit cell: (145.768, 146.832, 172.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 144 16.00 P 30 15.00 O 5870 8.00 N 5254 7.00 C 18857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.90 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 199 helices and 15 sheets defined 48.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.545A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 316 through 319 No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 330 through 345 removed outlier: 4.200A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 439 removed outlier: 4.506A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.712A pdb=" N SER A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.355A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 569 through 578 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 641 through 644 Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 694 through 718 Processing helix chain 'A' and resid 755 through 763 Processing helix chain 'A' and resid 771 through 788 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 220 through 235 removed outlier: 4.211A pdb=" N LEU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.929A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 319 No H-bonds generated for 'chain 'B' and resid 316 through 319' Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 330 through 345 removed outlier: 3.635A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.787A pdb=" N LYS B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 Processing helix chain 'B' and resid 418 through 439 removed outlier: 4.713A pdb=" N ASP B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 459 through 468 Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 493 through 508 removed outlier: 4.505A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Proline residue: B 506 - end of helix Processing helix chain 'B' and resid 510 through 516 Processing helix chain 'B' and resid 534 through 544 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 569 through 578 Processing helix chain 'B' and resid 589 through 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 641 through 644 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 683 through 689 Processing helix chain 'B' and resid 694 through 718 Processing helix chain 'B' and resid 755 through 764 removed outlier: 3.912A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 787 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 220 through 235 removed outlier: 4.278A pdb=" N LEU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 261 through 272 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 323 through 326 No H-bonds generated for 'chain 'C' and resid 323 through 326' Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.805A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.785A pdb=" N LYS C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 418 through 439 removed outlier: 4.525A pdb=" N ASP C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 493 through 508 removed outlier: 4.840A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 534 through 544 Processing helix chain 'C' and resid 554 through 562 Processing helix chain 'C' and resid 569 through 578 Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 641 through 644 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 683 through 689 Processing helix chain 'C' and resid 694 through 718 Processing helix chain 'C' and resid 755 through 764 removed outlier: 3.904A pdb=" N THR C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 787 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 220 through 235 removed outlier: 4.143A pdb=" N LEU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 237 through 243 Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 329 through 343 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 384 through 396 removed outlier: 3.878A pdb=" N LYS D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 418 through 439 removed outlier: 4.500A pdb=" N ASP D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 473 through 475 No H-bonds generated for 'chain 'D' and resid 473 through 475' Processing helix chain 'D' and resid 493 through 508 removed outlier: 4.337A pdb=" N TYR D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Proline residue: D 506 - end of helix Processing helix chain 'D' and resid 510 through 516 Processing helix chain 'D' and resid 534 through 544 Processing helix chain 'D' and resid 554 through 562 Processing helix chain 'D' and resid 569 through 578 Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 609 through 619 Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 641 through 644 Processing helix chain 'D' and resid 660 through 670 Processing helix chain 'D' and resid 683 through 688 Processing helix chain 'D' and resid 694 through 718 Processing helix chain 'D' and resid 755 through 763 Processing helix chain 'D' and resid 771 through 788 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 220 through 235 removed outlier: 4.257A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 261 through 272 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 291 through 305 Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 330 through 345 removed outlier: 4.177A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 367 No H-bonds generated for 'chain 'E' and resid 365 through 367' Processing helix chain 'E' and resid 384 through 396 removed outlier: 3.504A pdb=" N LYS E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 Processing helix chain 'E' and resid 418 through 439 removed outlier: 4.441A pdb=" N ASP E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.521A pdb=" N SER E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 467 Processing helix chain 'E' and resid 473 through 475 No H-bonds generated for 'chain 'E' and resid 473 through 475' Processing helix chain 'E' and resid 493 through 508 removed outlier: 4.220A pdb=" N TYR E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) Proline residue: E 506 - end of helix Processing helix chain 'E' and resid 510 through 516 Processing helix chain 'E' and resid 534 through 544 Processing helix chain 'E' and resid 554 through 561 Processing helix chain 'E' and resid 569 through 578 Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 609 through 620 Processing helix chain 'E' and resid 636 through 638 No H-bonds generated for 'chain 'E' and resid 636 through 638' Processing helix chain 'E' and resid 641 through 644 Processing helix chain 'E' and resid 660 through 670 Processing helix chain 'E' and resid 683 through 688 Processing helix chain 'E' and resid 694 through 718 Processing helix chain 'E' and resid 755 through 763 Processing helix chain 'E' and resid 771 through 786 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 220 through 235 removed outlier: 4.405A pdb=" N LEU F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 237 through 243 Processing helix chain 'F' and resid 261 through 272 Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 329 through 345 Processing helix chain 'F' and resid 365 through 367 No H-bonds generated for 'chain 'F' and resid 365 through 367' Processing helix chain 'F' and resid 384 through 396 removed outlier: 3.580A pdb=" N LYS F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 412 Processing helix chain 'F' and resid 418 through 439 removed outlier: 4.386A pdb=" N ASP F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 459 through 467 Processing helix chain 'F' and resid 473 through 475 No H-bonds generated for 'chain 'F' and resid 473 through 475' Processing helix chain 'F' and resid 493 through 508 removed outlier: 4.237A pdb=" N TYR F 505 " --> pdb=" O GLU F 501 " (cutoff:3.500A) Proline residue: F 506 - end of helix Processing helix chain 'F' and resid 510 through 516 Processing helix chain 'F' and resid 534 through 544 Processing helix chain 'F' and resid 554 through 561 Processing helix chain 'F' and resid 569 through 578 Processing helix chain 'F' and resid 589 through 591 No H-bonds generated for 'chain 'F' and resid 589 through 591' Processing helix chain 'F' and resid 609 through 619 Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 641 through 644 Processing helix chain 'F' and resid 660 through 671 Processing helix chain 'F' and resid 683 through 687 Processing helix chain 'F' and resid 694 through 718 Processing helix chain 'F' and resid 755 through 764 removed outlier: 4.135A pdb=" N THR F 764 " --> pdb=" O GLU F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 786 Processing helix chain 'G' and resid 117 through 124 Processing helix chain 'G' and resid 156 through 162 Processing helix chain 'G' and resid 169 through 179 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 242 through 255 removed outlier: 3.629A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 317 removed outlier: 3.987A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 363 Processing helix chain 'G' and resid 403 through 409 Processing helix chain 'G' and resid 459 through 462 Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 517 through 524 Processing helix chain 'G' and resid 527 through 536 Processing helix chain 'G' and resid 541 through 552 Processing helix chain 'G' and resid 557 through 565 Processing helix chain 'G' and resid 567 through 578 Processing helix chain 'H' and resid 244 through 252 Processing sheet with id= A, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.680A pdb=" N ALA A 309 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE A 354 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 311 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA A 356 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 313 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP A 314 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 279 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 651 through 654 removed outlier: 4.303A pdb=" N GLN A 651 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL A 524 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 629 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE A 526 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 631 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR A 582 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE A 630 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 584 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA A 632 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 586 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 375 through 379 removed outlier: 3.518A pdb=" N GLY B 255 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 651 through 654 removed outlier: 4.269A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL B 524 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 629 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE B 526 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY B 631 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 582 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE B 630 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 584 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ALA B 632 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 586 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 376 through 379 removed outlier: 8.297A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE C 379 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR C 254 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N VAL C 251 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 353 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N MET C 253 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA C 355 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY C 255 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR C 357 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 651 through 654 removed outlier: 4.129A pdb=" N GLN C 651 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL C 524 " --> pdb=" O VAL C 627 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL C 629 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE C 526 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY C 631 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE C 550 " --> pdb=" O PHE C 585 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 375 through 379 removed outlier: 3.887A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N VAL D 251 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL D 353 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N MET D 253 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA D 355 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLY D 255 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR D 357 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 651 through 654 removed outlier: 4.088A pdb=" N GLN D 651 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL D 524 " --> pdb=" O VAL D 627 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 629 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE D 526 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY D 631 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR D 582 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE D 630 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL D 584 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA D 632 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU D 586 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 353 through 357 Processing sheet with id= J, first strand: chain 'E' and resid 652 through 655 removed outlier: 8.552A pdb=" N ILE E 653 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU E 525 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL E 655 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR E 527 " --> pdb=" O VAL E 655 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL E 524 " --> pdb=" O VAL E 627 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL E 629 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE E 526 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY E 631 " --> pdb=" O PHE E 526 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLY E 528 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR E 633 " --> pdb=" O GLY E 528 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 375 through 379 removed outlier: 3.742A pdb=" N ARG F 375 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N VAL F 251 " --> pdb=" O VAL F 351 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL F 353 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N MET F 253 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA F 355 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N GLY F 255 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR F 357 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 651 through 654 removed outlier: 6.658A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F 550 " --> pdb=" O PHE F 585 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 224 through 226 removed outlier: 3.545A pdb=" N GLU G 451 " --> pdb=" O TYR G 439 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 467 through 470 removed outlier: 3.619A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL G 382 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N PHE G 326 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS G 384 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 422 through 424 1126 hydrogen bonds defined for protein. 3345 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: 10.24 Time building geometry restraints manager: 12.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10188 1.34 - 1.46: 4786 1.46 - 1.58: 15387 1.58 - 1.69: 48 1.69 - 1.81: 268 Bond restraints: 30677 Sorted by residual: bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP B 902 " pdb=" C5 ADP B 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP F 902 " pdb=" C5 ADP F 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 30672 not shown) Histogram of bond angle deviations from ideal: 98.05 - 106.44: 1147 106.44 - 114.82: 18401 114.82 - 123.20: 20797 123.20 - 131.58: 1105 131.58 - 139.96: 43 Bond angle restraints: 41493 Sorted by residual: angle pdb=" C1' ADP A 902 " pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " ideal model delta sigma weight residual 111.00 98.05 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C1' ADP E 902 " pdb=" C2' ADP E 902 " pdb=" C3' ADP E 902 " ideal model delta sigma weight residual 111.00 98.75 12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C1' ADP B 902 " pdb=" C2' ADP B 902 " pdb=" C3' ADP B 902 " ideal model delta sigma weight residual 111.00 99.60 11.40 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C1' ADP D 902 " pdb=" C2' ADP D 902 " pdb=" C3' ADP D 902 " ideal model delta sigma weight residual 111.00 100.69 10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " pdb=" C4' ADP A 902 " ideal model delta sigma weight residual 111.00 101.09 9.91 3.00e+00 1.11e-01 1.09e+01 ... (remaining 41488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 18737 35.31 - 70.61: 243 70.61 - 105.92: 8 105.92 - 141.23: 16 141.23 - 176.53: 4 Dihedral angle restraints: 19008 sinusoidal: 7963 harmonic: 11045 Sorted by residual: dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 116.54 -176.53 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PB ADP F 902 " pdb=" PA ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 148.77 151.23 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 88.57 -148.57 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 19005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4195 0.070 - 0.140: 411 0.140 - 0.210: 5 0.210 - 0.280: 9 0.280 - 0.349: 12 Chirality restraints: 4632 Sorted by residual: chirality pdb=" CA ASN G 510 " pdb=" N ASN G 510 " pdb=" C ASN G 510 " pdb=" CB ASN G 510 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' ATP D 901 " pdb=" C2' ATP D 901 " pdb=" C4' ATP D 901 " pdb=" O3' ATP D 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' ATP F 901 " pdb=" C1' ATP F 901 " pdb=" C3' ATP F 901 " pdb=" O2' ATP F 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4629 not shown) Planarity restraints: 5398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 505 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO E 506 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 506 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 506 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 505 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO B 506 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 506 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 506 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 505 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO A 506 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 506 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 506 " -0.019 5.00e-02 4.00e+02 ... (remaining 5395 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 322 2.59 - 3.17: 27120 3.17 - 3.74: 46053 3.74 - 4.32: 62826 4.32 - 4.90: 107107 Nonbonded interactions: 243428 Sorted by model distance: nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 2.011 2.440 nonbonded pdb=" OG SER G 417 " pdb=" O MET G 422 " model vdw 2.059 2.440 nonbonded pdb=" OG SER B 294 " pdb=" OE1 GLU G 436 " model vdw 2.078 2.440 nonbonded pdb=" OG1 THR F 458 " pdb=" OD1 ASP F 460 " model vdw 2.090 2.440 nonbonded pdb=" OG1 THR A 485 " pdb=" OD1 ASP A 487 " model vdw 2.117 2.440 ... (remaining 243423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'B' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'C' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'D' and (resid 208 through 787 or resid 901 through 902)) selection = chain 'E' selection = (chain 'F' and (resid 208 through 787 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.910 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 80.380 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.004 0.111 30677 Z= 0.259 Angle : 0.598 12.947 41493 Z= 0.275 Chirality : 0.045 0.349 4632 Planarity : 0.003 0.042 5398 Dihedral : 12.519 176.532 11860 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.93 % Allowed : 5.23 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.14), residues: 3767 helix: 2.04 (0.12), residues: 1910 sheet: -0.31 (0.24), residues: 458 loop : 0.44 (0.18), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 486 HIS 0.004 0.001 HIS G 528 PHE 0.011 0.001 PHE G 527 TYR 0.012 0.001 TYR G 172 ARG 0.003 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 521 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.6711 (mtm110) REVERT: B 209 ASN cc_start: 0.7312 (t0) cc_final: 0.6925 (t0) REVERT: C 571 ASP cc_start: 0.8101 (t0) cc_final: 0.7852 (t0) REVERT: D 785 LYS cc_start: 0.8354 (tmmt) cc_final: 0.8116 (tppt) REVERT: E 331 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7400 (mt-10) REVERT: E 709 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8681 (tp) REVERT: G 257 MET cc_start: 0.7102 (mmp) cc_final: 0.6844 (mmm) outliers start: 62 outliers final: 14 residues processed: 568 average time/residue: 1.7325 time to fit residues: 1119.9416 Evaluate side-chains 283 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 268 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 543 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 193 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 114 optimal weight: 0.0030 chunk 180 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS A 716 HIS B 651 GLN C 512 GLN C 638 GLN C 651 GLN C 716 HIS D 783 GLN E 361 ASN F 209 ASN F 470 ASN F 668 ASN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 HIS G 426 ASN ** G 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30677 Z= 0.177 Angle : 0.578 13.585 41493 Z= 0.273 Chirality : 0.042 0.199 4632 Planarity : 0.004 0.040 5398 Dihedral : 11.085 169.052 4434 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 2.96 % Allowed : 12.61 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.14), residues: 3767 helix: 2.02 (0.12), residues: 1911 sheet: -0.00 (0.24), residues: 446 loop : 0.47 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 561 HIS 0.010 0.001 HIS A 716 PHE 0.022 0.001 PHE B 464 TYR 0.018 0.001 TYR F 416 ARG 0.009 0.000 ARG B 775 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 296 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7237 (mtp) REVERT: A 480 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: A 609 ARG cc_start: 0.7267 (mtp-110) cc_final: 0.6552 (mtm110) REVERT: C 437 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7009 (ttp) REVERT: C 556 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7097 (mt-10) REVERT: D 398 MET cc_start: 0.8802 (mtp) cc_final: 0.8399 (ttm) REVERT: D 785 LYS cc_start: 0.8278 (tmmt) cc_final: 0.8071 (tppt) REVERT: E 229 MET cc_start: 0.6953 (tpt) cc_final: 0.5399 (tpt) REVERT: E 306 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7402 (m-40) REVERT: E 331 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7312 (mp0) REVERT: E 375 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.5265 (mtp85) REVERT: F 784 MET cc_start: 0.8000 (tpp) cc_final: 0.7706 (tpp) REVERT: G 206 ASN cc_start: 0.7242 (t0) cc_final: 0.7006 (t0) outliers start: 95 outliers final: 28 residues processed: 354 average time/residue: 1.5285 time to fit residues: 628.3800 Evaluate side-chains 288 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 255 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain H residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 233 optimal weight: 0.0170 chunk 94 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 371 optimal weight: 0.8980 chunk 306 optimal weight: 0.6980 chunk 341 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 432 GLN C 470 ASN C 512 GLN C 716 HIS E 670 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30677 Z= 0.191 Angle : 0.545 12.580 41493 Z= 0.258 Chirality : 0.041 0.159 4632 Planarity : 0.004 0.044 5398 Dihedral : 10.346 153.647 4423 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.87 % Allowed : 13.73 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.14), residues: 3767 helix: 1.90 (0.12), residues: 1921 sheet: 0.07 (0.24), residues: 454 loop : 0.46 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 561 HIS 0.009 0.001 HIS A 716 PHE 0.018 0.001 PHE B 464 TYR 0.016 0.001 TYR G 189 ARG 0.009 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 254 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7250 (mtp) REVERT: A 342 MET cc_start: 0.8522 (mmm) cc_final: 0.8100 (mmm) REVERT: A 480 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: B 672 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7529 (ptp90) REVERT: C 376 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: C 437 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7074 (ttp) REVERT: C 556 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 614 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8672 (tt) REVERT: D 264 MET cc_start: 0.8203 (mtp) cc_final: 0.7939 (mtp) REVERT: D 304 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: D 398 MET cc_start: 0.8878 (mtp) cc_final: 0.8418 (ttm) REVERT: D 785 LYS cc_start: 0.8328 (tmmt) cc_final: 0.8061 (tppt) REVERT: E 331 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7275 (mp0) REVERT: E 673 LYS cc_start: 0.8026 (pptt) cc_final: 0.7611 (tmmm) REVERT: F 253 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8366 (mtp) REVERT: F 784 MET cc_start: 0.7943 (tpp) cc_final: 0.7643 (tpp) REVERT: G 206 ASN cc_start: 0.7113 (t0) cc_final: 0.6880 (t0) REVERT: G 422 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7191 (mtp) REVERT: G 495 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6438 (mtp) outliers start: 92 outliers final: 44 residues processed: 322 average time/residue: 1.5061 time to fit residues: 565.9935 Evaluate side-chains 291 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 230 optimal weight: 0.1980 chunk 345 optimal weight: 3.9990 chunk 365 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 327 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS C 470 ASN C 512 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30677 Z= 0.179 Angle : 0.527 11.558 41493 Z= 0.250 Chirality : 0.041 0.159 4632 Planarity : 0.004 0.045 5398 Dihedral : 9.816 143.808 4421 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 3.33 % Allowed : 13.92 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.14), residues: 3767 helix: 1.88 (0.12), residues: 1920 sheet: 0.26 (0.24), residues: 446 loop : 0.41 (0.18), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 561 HIS 0.006 0.001 HIS A 716 PHE 0.014 0.001 PHE B 464 TYR 0.014 0.001 TYR A 416 ARG 0.003 0.000 ARG B 635 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 257 time to evaluate : 3.758 Fit side-chains revert: symmetry clash REVERT: A 229 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7249 (mtp) REVERT: A 480 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: A 556 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: B 476 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: B 672 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7475 (ptp-170) REVERT: C 376 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: C 437 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7139 (ttp) REVERT: D 264 MET cc_start: 0.8230 (mtp) cc_final: 0.7914 (mtp) REVERT: D 304 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: D 398 MET cc_start: 0.8903 (mtp) cc_final: 0.8479 (ttm) REVERT: D 785 LYS cc_start: 0.8339 (tmmt) cc_final: 0.8051 (tppt) REVERT: E 298 LYS cc_start: 0.8453 (tmmt) cc_final: 0.8221 (tttm) REVERT: E 306 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: E 331 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7241 (mp0) REVERT: E 437 MET cc_start: 0.7972 (ttp) cc_final: 0.7707 (ttt) REVERT: E 673 LYS cc_start: 0.8032 (pptt) cc_final: 0.7598 (tmmm) REVERT: F 342 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8142 (mmt) REVERT: F 427 GLU cc_start: 0.7309 (tt0) cc_final: 0.6958 (tt0) REVERT: F 571 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: G 122 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8394 (mm) REVERT: G 206 ASN cc_start: 0.7169 (t0) cc_final: 0.6930 (t0) REVERT: G 495 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6437 (mtp) outliers start: 107 outliers final: 50 residues processed: 334 average time/residue: 1.4744 time to fit residues: 574.6609 Evaluate side-chains 299 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 236 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 665 SER Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 4.9990 chunk 207 optimal weight: 0.0020 chunk 5 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 311 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS B 270 ASN C 512 GLN D 394 HIS D 509 HIS G 289 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30677 Z= 0.297 Angle : 0.571 13.316 41493 Z= 0.274 Chirality : 0.043 0.190 4632 Planarity : 0.004 0.047 5398 Dihedral : 9.697 146.215 4421 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 3.46 % Allowed : 14.86 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.14), residues: 3767 helix: 1.73 (0.12), residues: 1922 sheet: 0.21 (0.24), residues: 454 loop : 0.38 (0.18), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 561 HIS 0.011 0.001 HIS A 716 PHE 0.016 0.002 PHE C 573 TYR 0.017 0.001 TYR A 416 ARG 0.010 0.000 ARG A 717 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 241 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7234 (mtp) REVERT: A 480 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: A 556 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: B 264 MET cc_start: 0.8192 (mtt) cc_final: 0.7983 (mtt) REVERT: C 376 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: C 614 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8715 (tt) REVERT: D 283 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: D 304 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: D 412 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: D 785 LYS cc_start: 0.8358 (tmmt) cc_final: 0.8079 (tppt) REVERT: E 298 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8306 (tttm) REVERT: E 306 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7375 (m-40) REVERT: E 396 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8366 (ttmm) REVERT: E 437 MET cc_start: 0.7972 (ttp) cc_final: 0.7712 (ttt) REVERT: F 342 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8142 (mmt) REVERT: F 427 GLU cc_start: 0.7390 (tt0) cc_final: 0.7149 (tt0) REVERT: G 122 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8370 (mm) REVERT: G 206 ASN cc_start: 0.7204 (t0) cc_final: 0.6951 (t0) REVERT: G 495 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6496 (mtp) outliers start: 111 outliers final: 52 residues processed: 331 average time/residue: 1.4194 time to fit residues: 550.7448 Evaluate side-chains 294 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 229 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 365 optimal weight: 0.7980 chunk 303 optimal weight: 6.9990 chunk 169 optimal weight: 0.0040 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS C 512 GLN E 670 GLN F 470 ASN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30677 Z= 0.176 Angle : 0.540 12.304 41493 Z= 0.255 Chirality : 0.041 0.270 4632 Planarity : 0.004 0.047 5398 Dihedral : 9.398 147.580 4421 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 3.02 % Allowed : 15.63 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 3767 helix: 1.81 (0.12), residues: 1920 sheet: 0.33 (0.24), residues: 447 loop : 0.34 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 561 HIS 0.003 0.001 HIS G 528 PHE 0.012 0.001 PHE F 573 TYR 0.013 0.001 TYR F 416 ARG 0.007 0.000 ARG B 635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 236 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7234 (mtp) REVERT: A 480 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: A 556 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: B 560 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7008 (mtt) REVERT: C 376 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: C 614 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8657 (tt) REVERT: D 264 MET cc_start: 0.8192 (mtp) cc_final: 0.7971 (mtp) REVERT: D 304 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: D 398 MET cc_start: 0.8978 (mtp) cc_final: 0.8549 (ttm) REVERT: D 709 ILE cc_start: 0.8664 (tt) cc_final: 0.8420 (tt) REVERT: D 785 LYS cc_start: 0.8335 (tmmt) cc_final: 0.8051 (tppt) REVERT: E 298 LYS cc_start: 0.8444 (tmmt) cc_final: 0.8211 (tttm) REVERT: E 302 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: E 306 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7341 (m-40) REVERT: E 331 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6716 (mt-10) REVERT: E 396 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8368 (ttmm) REVERT: E 437 MET cc_start: 0.7928 (ttp) cc_final: 0.7714 (ttt) REVERT: F 342 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8089 (mmt) REVERT: F 571 ASP cc_start: 0.8332 (t0) cc_final: 0.8074 (m-30) REVERT: G 122 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8412 (mm) REVERT: G 206 ASN cc_start: 0.7221 (t0) cc_final: 0.6988 (t0) REVERT: G 289 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.6507 (pp30) REVERT: G 495 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6447 (mtp) outliers start: 97 outliers final: 51 residues processed: 310 average time/residue: 1.5436 time to fit residues: 555.9861 Evaluate side-chains 291 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 chunk 267 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 364 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 168 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS C 512 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30677 Z= 0.178 Angle : 0.531 11.608 41493 Z= 0.251 Chirality : 0.041 0.246 4632 Planarity : 0.004 0.047 5398 Dihedral : 9.141 148.191 4419 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 2.90 % Allowed : 15.91 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.14), residues: 3767 helix: 1.84 (0.12), residues: 1914 sheet: 0.42 (0.24), residues: 447 loop : 0.33 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 561 HIS 0.013 0.001 HIS A 716 PHE 0.011 0.001 PHE B 464 TYR 0.013 0.001 TYR G 189 ARG 0.009 0.000 ARG B 635 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 238 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7238 (mtp) REVERT: A 480 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: A 556 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: B 560 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6954 (mtt) REVERT: C 376 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: C 556 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7125 (mt-10) REVERT: D 264 MET cc_start: 0.8204 (mtp) cc_final: 0.7949 (mtp) REVERT: D 304 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: D 398 MET cc_start: 0.8976 (mtp) cc_final: 0.8538 (ttm) REVERT: D 709 ILE cc_start: 0.8638 (tt) cc_final: 0.8390 (tt) REVERT: D 785 LYS cc_start: 0.8391 (tmmt) cc_final: 0.8114 (tppt) REVERT: E 298 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8212 (tttm) REVERT: E 302 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7179 (tp30) REVERT: E 306 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7330 (m-40) REVERT: E 331 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6714 (mt-10) REVERT: E 396 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8367 (ttmm) REVERT: E 437 MET cc_start: 0.7912 (ttp) cc_final: 0.7706 (ttt) REVERT: F 253 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: F 342 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8092 (mmt) REVERT: F 571 ASP cc_start: 0.8328 (t0) cc_final: 0.8086 (m-30) REVERT: G 206 ASN cc_start: 0.7225 (t0) cc_final: 0.7002 (t0) REVERT: G 495 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6563 (mtp) outliers start: 93 outliers final: 51 residues processed: 309 average time/residue: 1.4824 time to fit residues: 535.7213 Evaluate side-chains 289 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 225 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.1980 chunk 145 optimal weight: 0.6980 chunk 217 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 286 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS C 512 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30677 Z= 0.186 Angle : 0.536 11.440 41493 Z= 0.254 Chirality : 0.041 0.234 4632 Planarity : 0.004 0.047 5398 Dihedral : 8.890 145.951 4417 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 2.65 % Allowed : 16.44 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.14), residues: 3767 helix: 1.87 (0.12), residues: 1910 sheet: 0.43 (0.24), residues: 449 loop : 0.32 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 561 HIS 0.004 0.001 HIS A 716 PHE 0.012 0.001 PHE F 573 TYR 0.013 0.001 TYR F 416 ARG 0.013 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 240 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7242 (mtp) REVERT: A 556 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: B 560 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7202 (mtt) REVERT: C 264 MET cc_start: 0.7776 (mtt) cc_final: 0.7456 (mtt) REVERT: C 376 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: D 264 MET cc_start: 0.8234 (mtp) cc_final: 0.7958 (mtp) REVERT: D 304 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6978 (tt0) REVERT: D 709 ILE cc_start: 0.8642 (tt) cc_final: 0.8391 (tt) REVERT: D 785 LYS cc_start: 0.8393 (tmmt) cc_final: 0.8086 (tppt) REVERT: E 298 LYS cc_start: 0.8466 (tmmt) cc_final: 0.8236 (tttm) REVERT: E 302 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: E 306 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7192 (m-40) REVERT: E 331 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6687 (mt-10) REVERT: E 396 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8370 (ttmm) REVERT: E 437 MET cc_start: 0.7909 (ttp) cc_final: 0.7708 (ttt) REVERT: F 253 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8220 (mtp) REVERT: F 571 ASP cc_start: 0.8324 (t0) cc_final: 0.8096 (m-30) REVERT: G 289 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: G 495 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6582 (mtp) REVERT: H 253 ASN cc_start: 0.6715 (m-40) cc_final: 0.6484 (m-40) outliers start: 85 outliers final: 52 residues processed: 307 average time/residue: 1.5214 time to fit residues: 546.5767 Evaluate side-chains 288 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 224 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 0.8980 chunk 349 optimal weight: 0.0060 chunk 318 optimal weight: 2.9990 chunk 339 optimal weight: 0.6980 chunk 348 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 321 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS C 512 GLN G 206 ASN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30677 Z= 0.176 Angle : 0.550 11.342 41493 Z= 0.260 Chirality : 0.041 0.231 4632 Planarity : 0.004 0.047 5398 Dihedral : 8.747 142.998 4417 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 2.43 % Allowed : 17.10 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.14), residues: 3767 helix: 1.89 (0.12), residues: 1910 sheet: 0.48 (0.24), residues: 448 loop : 0.33 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 561 HIS 0.021 0.001 HIS A 716 PHE 0.011 0.001 PHE B 464 TYR 0.012 0.001 TYR F 416 ARG 0.014 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 238 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7202 (mtp) REVERT: A 556 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: B 560 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7133 (mtt) REVERT: C 376 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: D 264 MET cc_start: 0.8220 (mtp) cc_final: 0.7955 (mtp) REVERT: D 304 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: D 709 ILE cc_start: 0.8640 (tt) cc_final: 0.8391 (tt) REVERT: D 785 LYS cc_start: 0.8403 (tmmt) cc_final: 0.8091 (tppt) REVERT: E 298 LYS cc_start: 0.8448 (tmmt) cc_final: 0.8212 (tttm) REVERT: E 306 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7203 (m-40) REVERT: E 331 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6691 (mt-10) REVERT: E 396 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8368 (ttmm) REVERT: F 253 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8183 (mtp) REVERT: F 571 ASP cc_start: 0.8319 (t0) cc_final: 0.8094 (m-30) REVERT: G 206 ASN cc_start: 0.7011 (OUTLIER) cc_final: 0.6802 (t0) REVERT: G 289 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: G 495 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6571 (mtp) REVERT: H 253 ASN cc_start: 0.6711 (m-40) cc_final: 0.6489 (m-40) outliers start: 78 outliers final: 48 residues processed: 297 average time/residue: 1.4323 time to fit residues: 496.5314 Evaluate side-chains 285 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 225 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 249 optimal weight: 0.8980 chunk 376 optimal weight: 0.0370 chunk 346 optimal weight: 0.9990 chunk 299 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS C 512 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30677 Z= 0.189 Angle : 0.559 10.967 41493 Z= 0.264 Chirality : 0.041 0.228 4632 Planarity : 0.004 0.048 5398 Dihedral : 8.620 139.757 4417 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.27 % Allowed : 17.35 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.14), residues: 3767 helix: 1.91 (0.12), residues: 1910 sheet: 0.46 (0.24), residues: 450 loop : 0.33 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 561 HIS 0.004 0.001 HIS G 205 PHE 0.015 0.001 PHE D 276 TYR 0.012 0.001 TYR F 416 ARG 0.017 0.000 ARG B 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 233 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7200 (mtp) REVERT: A 556 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: B 560 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7123 (mtt) REVERT: C 264 MET cc_start: 0.7776 (mtt) cc_final: 0.7489 (mtt) REVERT: C 376 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: D 264 MET cc_start: 0.8224 (mtp) cc_final: 0.7946 (mtp) REVERT: D 304 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: D 412 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: D 709 ILE cc_start: 0.8636 (tt) cc_final: 0.8388 (tt) REVERT: D 785 LYS cc_start: 0.8431 (tmmt) cc_final: 0.8111 (tppt) REVERT: E 298 LYS cc_start: 0.8462 (tmmt) cc_final: 0.8246 (tttm) REVERT: E 306 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7211 (m-40) REVERT: E 331 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: E 396 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8368 (ttmm) REVERT: F 253 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8223 (mtp) REVERT: F 571 ASP cc_start: 0.8315 (t0) cc_final: 0.8095 (m-30) REVERT: G 289 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: G 495 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6677 (mtp) REVERT: H 253 ASN cc_start: 0.6726 (m-40) cc_final: 0.6513 (m-40) outliers start: 73 outliers final: 53 residues processed: 291 average time/residue: 1.4885 time to fit residues: 505.9926 Evaluate side-chains 292 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 227 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 1.9990 chunk 238 optimal weight: 0.0970 chunk 319 optimal weight: 6.9990 chunk 91 optimal weight: 0.0970 chunk 276 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 308 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090035 restraints weight = 47349.894| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.64 r_work: 0.3066 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.287 30677 Z= 0.238 Angle : 0.704 65.898 41493 Z= 0.395 Chirality : 0.058 2.778 4632 Planarity : 0.006 0.268 5398 Dihedral : 8.623 139.749 4417 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.21 % Allowed : 17.53 % Favored : 80.26 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.14), residues: 3767 helix: 1.90 (0.12), residues: 1910 sheet: 0.46 (0.24), residues: 450 loop : 0.33 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 561 HIS 0.332 0.004 HIS A 716 PHE 0.015 0.001 PHE D 276 TYR 0.012 0.001 TYR F 416 ARG 0.010 0.000 ARG B 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9767.76 seconds wall clock time: 173 minutes 44.22 seconds (10424.22 seconds total)