Starting phenix.real_space_refine on Fri Mar 22 18:36:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dau_27276/03_2024/8dau_27276_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dau_27276/03_2024/8dau_27276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dau_27276/03_2024/8dau_27276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dau_27276/03_2024/8dau_27276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dau_27276/03_2024/8dau_27276_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dau_27276/03_2024/8dau_27276_updated.pdb" } resolution = 3.7 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= -0.017 sd= 1.101 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 29 5.49 5 S 156 5.16 5 C 21438 2.51 5 N 5955 2.21 5 O 6668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34248 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5555 Classifications: {'peptide': 712} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 5599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5599 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 680} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4311 Classifications: {'peptide': 555} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 525} Chain breaks: 4 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4240 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 517} Chain breaks: 5 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4113 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 502} Chain breaks: 3 Chain: "F" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4284 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 521} Chain breaks: 5 Chain: "G" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3825 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 453} Chain: "H" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 477 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain breaks: 1 Chain: "I" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 298 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} 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 28365 SG CYS G 137 46.667 49.266 94.291 1.00108.38 S ATOM 28425 SG CYS G 145 50.351 49.983 94.351 1.00 88.12 S ATOM 28452 SG CYS G 148 48.238 50.081 97.410 1.00 87.79 S ATOM 28922 SG CYS G 204 74.888 91.352 115.516 1.00102.01 S ATOM 29020 SG CYS G 216 75.252 90.917 111.812 1.00 87.55 S ATOM 29041 SG CYS G 219 72.449 92.854 113.118 1.00 90.95 S Time building chain proxies: 16.91, per 1000 atoms: 0.49 Number of scatterers: 34248 At special positions: 0 Unit cell: (151.088, 169.176, 191.52, 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 156 16.00 P 29 15.00 O 6668 8.00 N 5955 7.00 C 21438 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: 13.92 Conformation dependent library (CDL) restraints added in 5.7 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 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 208 helices and 22 sheets defined 45.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.32 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.556A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 141 through 148 removed outlier: 4.218A pdb=" N LYS A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 202 through 207 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 220 through 235 removed outlier: 4.344A 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 237 through 243 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 291 through 305 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 329 through 344 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.730A pdb=" N LYS A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 439 removed outlier: 4.389A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.504A 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 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.386A 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 516 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 592 removed outlier: 3.585A pdb=" N ILE A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 592' Processing helix chain 'A' and resid 609 through 620 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 687 Processing helix chain 'A' and resid 694 through 717 Processing helix chain 'A' and resid 755 through 763 Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 96 through 102 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.742A pdb=" N LYS B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 203 through 206 No H-bonds generated for 'chain 'B' and resid 203 through 206' 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: 4.808A 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 237 through 243 Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 292 through 305 Processing helix 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 344 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 394 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 418 through 439 removed outlier: 4.040A pdb=" N ASP B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 5.437A 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: 4.397A 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 536 through 544 Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 569 through 578 Processing helix chain 'B' and resid 589 through 592 Processing helix chain 'B' and resid 609 through 620 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 688 Processing helix chain 'B' and resid 694 through 717 Processing helix chain 'B' and resid 755 through 763 Processing helix chain 'B' and resid 771 through 785 Processing helix chain 'C' and resid 96 through 102 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 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 237 through 243 removed outlier: 3.555A pdb=" N LYS C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 272 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 291 through 305 Processing helix chain 'C' and resid 316 through 319 No H-bonds generated for 'chain 'C' and resid 316 through 319' Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.643A 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 368 Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.775A 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: 4.195A pdb=" N ASP C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 5.568A 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 468 Processing helix chain 'C' and resid 493 through 508 removed outlier: 3.976A pdb=" N GLU C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 4.391A 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 545 Processing helix chain 'C' and resid 554 through 562 Processing helix chain 'C' and resid 569 through 578 Processing helix chain 'C' and resid 589 through 592 No H-bonds generated for 'chain 'C' and resid 589 through 592' Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 641 through 644 No H-bonds generated for 'chain 'C' and resid 641 through 644' Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 683 through 688 Processing helix chain 'C' and resid 694 through 717 Processing helix chain 'C' and resid 755 through 764 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'D' and resid 98 through 102 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 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 282 through 285 No H-bonds generated for 'chain 'D' and resid 282 through 285' Processing helix chain 'D' and resid 289 through 305 Processing helix chain 'D' and resid 316 through 319 No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 329 through 344 Processing helix chain 'D' and resid 365 through 368 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 418 through 437 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 459 through 468 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 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 493 through 508 removed outlier: 4.771A 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 545 removed outlier: 3.519A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 562 removed outlier: 4.332A pdb=" N SER D 559 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 578 Processing helix chain 'D' and resid 589 through 592 Processing helix chain 'D' and resid 608 through 619 Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' 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 717 removed outlier: 3.500A pdb=" N LEU D 698 " --> pdb=" O GLY D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 764 Processing helix chain 'D' and resid 771 through 785 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: 3.760A 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 238 through 243 Processing helix chain 'E' and resid 261 through 272 Processing helix chain 'E' and resid 281 through 287 removed outlier: 3.714A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 306 Processing helix chain 'E' and resid 316 through 319 No H-bonds generated for 'chain 'E' and resid 316 through 319' Processing helix chain 'E' and resid 331 through 344 removed outlier: 3.503A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 368 removed outlier: 3.572A pdb=" N ARG E 368 " --> pdb=" O PRO E 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 368' Processing helix chain 'E' and resid 384 through 394 Processing helix chain 'E' and resid 406 through 412 Processing helix chain 'E' and resid 418 through 439 removed outlier: 4.713A pdb=" N ASP E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 459 through 467 Processing helix chain 'E' and resid 486 through 488 No H-bonds generated for 'chain 'E' and resid 486 through 488' Processing helix chain 'E' and resid 493 through 508 removed outlier: 4.229A 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 515 Processing helix chain 'E' and resid 536 through 544 Processing helix chain 'E' and resid 554 through 562 Processing helix chain 'E' and resid 569 through 578 Processing helix chain 'E' and resid 589 through 592 Processing helix chain 'E' and resid 608 through 619 Processing helix chain 'E' and resid 641 through 644 Processing helix chain 'E' and resid 660 through 672 Processing helix chain 'E' and resid 682 through 688 removed outlier: 3.923A pdb=" N ALA E 688 " --> pdb=" O ALA E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 717 Processing helix chain 'E' and resid 755 through 763 Processing helix chain 'E' and resid 771 through 785 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 202 through 206 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: 3.915A 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 286 Processing helix chain 'F' and resid 291 through 306 Processing helix chain 'F' and resid 316 through 319 No H-bonds generated for 'chain 'F' and resid 316 through 319' Processing helix chain 'F' and resid 329 through 343 removed outlier: 3.841A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 368 Processing helix chain 'F' and resid 384 through 394 Processing helix chain 'F' and resid 406 through 412 Processing helix chain 'F' and resid 418 through 437 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 459 through 468 Processing helix chain 'F' and resid 486 through 488 No H-bonds generated for 'chain 'F' and resid 486 through 488' Processing helix chain 'F' and resid 493 through 508 removed outlier: 4.616A 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 562 Processing helix chain 'F' and resid 569 through 578 Processing helix chain 'F' and resid 589 through 592 removed outlier: 3.863A pdb=" N ILE F 592 " --> pdb=" O LEU F 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 589 through 592' Processing helix chain 'F' and resid 609 through 620 Processing helix chain 'F' and resid 641 through 644 Processing helix chain 'F' and resid 660 through 673 removed outlier: 5.038A pdb=" N LYS F 673 " --> pdb=" O ALA F 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 689 Processing helix chain 'F' and resid 694 through 717 Processing helix chain 'F' and resid 755 through 763 Processing helix chain 'F' and resid 771 through 785 Processing helix chain 'G' and resid 117 through 123 Processing helix chain 'G' and resid 156 through 162 Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.733A pdb=" N TYR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) 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 253 removed outlier: 3.982A pdb=" N ALA G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 317 removed outlier: 3.776A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 364 Processing helix chain 'G' and resid 403 through 411 removed outlier: 3.826A pdb=" N THR G 410 " --> pdb=" O GLU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 462 No H-bonds generated for 'chain 'G' and resid 460 through 462' Processing helix chain 'G' and resid 501 through 512 Processing helix chain 'G' and resid 517 through 523 Processing helix chain 'G' and resid 527 through 536 Processing helix chain 'G' and resid 541 through 552 Processing helix chain 'G' and resid 556 through 565 Processing helix chain 'G' and resid 567 through 578 Processing helix chain 'H' and resid 244 through 253 removed outlier: 3.754A pdb=" N ARG H 252 " --> pdb=" O ALA H 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 30 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 156 through 159 No H-bonds generated for 'chain 'J' and resid 156 through 159' Processing helix chain 'K' and resid 223 through 234 Processing helix chain 'K' and resid 238 through 240 No H-bonds generated for 'chain 'K' and resid 238 through 240' Processing helix chain 'K' and resid 256 through 259 No H-bonds generated for 'chain 'K' and resid 256 through 259' Processing sheet with id= A, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.027A pdb=" N ILE A 80 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 51 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A 82 " --> pdb=" O ILE A 51 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= C, first strand: chain 'A' and resid 191 through 193 removed outlier: 7.273A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 275 through 280 removed outlier: 3.652A pdb=" N PHE A 312 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 356 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 357 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU A 252 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A 376 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR A 254 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP A 378 " --> pdb=" O TYR A 254 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 548 through 552 removed outlier: 3.788A pdb=" N GLY A 528 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 525 " --> pdb=" O ASP A 650 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A 652 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 527 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR A 654 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.569A pdb=" N ILE B 80 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE B 51 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 82 " --> pdb=" O ILE B 51 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= H, first strand: chain 'B' and resid 191 through 193 removed outlier: 7.135A pdb=" N LEU B 127 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 175 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 375 through 379 removed outlier: 8.551A pdb=" N VAL B 251 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 353 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N MET B 253 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 355 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY B 255 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.727A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 629 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N PHE B 526 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY B 631 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N GLY B 528 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE B 630 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL B 584 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA B 632 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 586 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP B 587 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 552 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 375 through 379 removed outlier: 3.637A pdb=" N THR C 357 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE C 277 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 524 through 528 removed outlier: 6.717A pdb=" N GLN C 651 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR C 527 " --> pdb=" O GLN C 651 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 653 " --> pdb=" O TYR C 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 375 through 379 removed outlier: 4.171A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N VAL D 251 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 353 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N MET D 253 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA D 355 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY D 255 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR D 357 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 651 through 655 removed outlier: 6.798A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL D 552 " --> pdb=" O ASP D 587 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 375 through 379 removed outlier: 8.846A pdb=" N VAL E 251 " --> pdb=" O VAL E 351 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL E 353 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET E 253 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA E 355 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY E 255 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N THR E 357 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA E 309 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE E 354 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE E 311 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA E 356 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE E 313 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE E 275 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE E 312 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE E 277 " --> pdb=" O PHE E 312 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 651 through 654 removed outlier: 9.180A pdb=" N VAL E 524 " --> pdb=" O VAL E 627 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 629 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE E 526 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY E 631 " --> pdb=" O PHE E 526 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 375 through 379 removed outlier: 8.582A pdb=" N VAL F 251 " --> pdb=" O VAL F 351 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL F 353 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET F 253 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA F 355 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLY F 255 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR F 357 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 352 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 651 through 655 removed outlier: 9.054A pdb=" N VAL F 524 " --> pdb=" O VAL F 627 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL F 629 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE F 526 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY F 631 " --> pdb=" O PHE F 526 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY F 528 " --> pdb=" O GLY F 631 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR F 633 " --> pdb=" O GLY F 528 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN F 548 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE F 585 " --> pdb=" O ASN F 548 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE F 550 " --> pdb=" O PHE F 585 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP F 587 " --> pdb=" O ILE F 550 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL F 552 " --> pdb=" O ASP F 587 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 467 through 470 removed outlier: 3.506A pdb=" N GLY G 469 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE G 239 " --> pdb=" O GLY G 469 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG G 259 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL G 382 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N PHE G 326 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS G 384 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 422 through 424 Processing sheet with id= U, first strand: chain 'J' and resid 113 through 116 removed outlier: 3.539A pdb=" N LEU J 169 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 212 through 215 1257 hydrogen bonds defined for protein. 3651 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: 12.02 Time building geometry restraints manager: 15.04 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: 11581 1.34 - 1.46: 6344 1.46 - 1.58: 16565 1.58 - 1.70: 41 1.70 - 1.81: 288 Bond restraints: 34819 Sorted by residual: bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " 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 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 3.01e+01 bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP B 902 " pdb=" C5 ADP B 902 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 34814 not shown) Histogram of bond angle deviations from ideal: 99.37 - 109.53: 2951 109.53 - 119.69: 27596 119.69 - 129.85: 16406 129.85 - 140.01: 154 140.01 - 150.17: 4 Bond angle restraints: 47111 Sorted by residual: angle pdb=" C ARG B 672 " pdb=" N LYS B 673 " pdb=" CA LYS B 673 " ideal model delta sigma weight residual 120.29 137.43 -17.14 1.42e+00 4.96e-01 1.46e+02 angle pdb=" C ILE E 639 " pdb=" N ASP E 640 " pdb=" CA ASP E 640 " ideal model delta sigma weight residual 121.80 150.17 -28.37 2.44e+00 1.68e-01 1.35e+02 angle pdb=" C PRO E 248 " pdb=" N ARG E 249 " pdb=" CA ARG E 249 " ideal model delta sigma weight residual 122.58 144.72 -22.14 2.07e+00 2.33e-01 1.14e+02 angle pdb=" C GLU E 331 " pdb=" N ARG E 332 " pdb=" CA ARG E 332 " ideal model delta sigma weight residual 121.54 141.02 -19.48 1.91e+00 2.74e-01 1.04e+02 angle pdb=" C ILE B 94 " pdb=" N ASN B 95 " pdb=" CA ASN B 95 " ideal model delta sigma weight residual 121.06 139.86 -18.80 1.88e+00 2.83e-01 1.00e+02 ... (remaining 47106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 21269 33.12 - 66.24: 234 66.24 - 99.36: 26 99.36 - 132.48: 15 132.48 - 165.60: 4 Dihedral angle restraints: 21548 sinusoidal: 9006 harmonic: 12542 Sorted by residual: dihedral pdb=" CA ALA F 307 " pdb=" C ALA F 307 " pdb=" N PRO F 308 " pdb=" CA PRO F 308 " ideal model delta harmonic sigma weight residual 180.00 137.48 42.52 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" C2' ADP E 901 " pdb=" C1' ADP E 901 " pdb=" N9 ADP E 901 " pdb=" C4 ADP E 901 " ideal model delta sinusoidal sigma weight residual 91.55 -102.85 -165.60 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual 300.00 153.20 146.81 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 21545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 5166 0.344 - 0.688: 76 0.688 - 1.033: 0 1.033 - 1.377: 5 1.377 - 1.721: 59 Chirality restraints: 5306 Sorted by residual: chirality pdb=" CG LEU E 367 " pdb=" CB LEU E 367 " pdb=" CD1 LEU E 367 " pdb=" CD2 LEU E 367 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CG LEU A 79 " pdb=" CB LEU A 79 " pdb=" CD1 LEU A 79 " pdb=" CD2 LEU A 79 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU E 586 " pdb=" CB LEU E 586 " pdb=" CD1 LEU E 586 " pdb=" CD2 LEU E 586 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 ... (remaining 5303 not shown) Planarity restraints: 6138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 329 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C GLU B 329 " -0.032 2.00e-02 2.50e+03 pdb=" O GLU B 329 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL B 330 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 294 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C SER F 294 " -0.028 2.00e-02 2.50e+03 pdb=" O SER F 294 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN F 295 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 506 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C LYS G 506 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS G 506 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR G 507 " 0.009 2.00e-02 2.50e+03 ... (remaining 6135 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 15 2.07 - 2.78: 7604 2.78 - 3.49: 52073 3.49 - 4.19: 75442 4.19 - 4.90: 136020 Nonbonded interactions: 271154 Sorted by model distance: nonbonded pdb=" NZ LYS J 148 " pdb=" C GLY K 276 " model vdw 1.366 3.350 nonbonded pdb=" NZ LYS I 48 " pdb=" C GLY J 176 " model vdw 1.378 3.350 nonbonded pdb=" OG1 THR D 754 " pdb=" OE1 GLU D 756 " model vdw 1.924 2.440 nonbonded pdb=" OG SER D 559 " pdb=" O GLU D 564 " model vdw 1.925 2.440 nonbonded pdb=" OD1 ASP B 590 " pdb=" OG1 THR B 633 " model vdw 1.954 2.440 ... (remaining 271149 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 33 through 440 or resid 447 through 786 or resid 901 throu \ gh 902)) selection = (chain 'B' and (resid 33 through 786 or resid 901 through 902)) } ncs_group { reference = (chain 'C' and (resid 207 through 440 or resid 447 through 786 or resid 902)) selection = (chain 'D' and (resid 207 through 786 or resid 902)) selection = (chain 'E' and (resid 207 through 786 or resid 902)) selection = (chain 'F' and (resid 207 through 786 or resid 902)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 13.110 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 93.570 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 34819 Z= 0.229 Angle : 0.930 28.372 47111 Z= 0.471 Chirality : 0.184 1.721 5306 Planarity : 0.003 0.036 6138 Dihedral : 11.503 165.603 13424 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 0.90 % Allowed : 4.51 % Favored : 94.59 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.69 (0.14), residues: 4274 helix: 2.39 (0.12), residues: 2004 sheet: 0.13 (0.23), residues: 530 loop : -0.03 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 489 HIS 0.004 0.001 HIS C 757 PHE 0.009 0.001 PHE C 275 TYR 0.020 0.001 TYR G 507 ARG 0.002 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 591 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.6283 (mm) cc_final: 0.5926 (mm) REVERT: A 151 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8734 (mm-30) REVERT: A 194 TRP cc_start: 0.1698 (p90) cc_final: 0.0334 (t60) REVERT: A 208 MET cc_start: 0.8145 (tmm) cc_final: 0.7929 (tmm) REVERT: A 405 ASP cc_start: 0.8347 (t70) cc_final: 0.8091 (t0) REVERT: B 65 ASP cc_start: 0.4621 (OUTLIER) cc_final: 0.3981 (m-30) REVERT: B 183 TYR cc_start: 0.7170 (p90) cc_final: 0.6779 (p90) REVERT: B 332 ARG cc_start: 0.6720 (mtm110) cc_final: 0.6280 (mtt180) REVERT: B 483 ASN cc_start: 0.8564 (t0) cc_final: 0.8267 (p0) REVERT: B 588 GLU cc_start: 0.8363 (tt0) cc_final: 0.8058 (tm-30) REVERT: B 778 GLU cc_start: 0.8511 (mp0) cc_final: 0.8232 (mm-30) REVERT: C 317 ASP cc_start: 0.7908 (p0) cc_final: 0.7633 (t0) REVERT: C 342 MET cc_start: 0.8525 (tpp) cc_final: 0.8131 (mmm) REVERT: C 348 ARG cc_start: 0.8586 (mtt90) cc_final: 0.7597 (mmm160) REVERT: C 561 TRP cc_start: 0.6281 (t60) cc_final: 0.6028 (t60) REVERT: C 570 ARG cc_start: 0.8219 (mmm160) cc_final: 0.6966 (tpp80) REVERT: C 608 ASP cc_start: 0.5783 (m-30) cc_final: 0.5575 (m-30) REVERT: C 649 LEU cc_start: 0.9076 (mm) cc_final: 0.8749 (tp) REVERT: D 402 ASP cc_start: 0.7841 (m-30) cc_final: 0.7557 (p0) REVERT: E 409 LEU cc_start: 0.9163 (mt) cc_final: 0.8465 (mt) REVERT: E 430 MET cc_start: 0.8180 (tpp) cc_final: 0.7901 (ttp) REVERT: E 560 MET cc_start: 0.5852 (mpp) cc_final: 0.5484 (mpp) REVERT: E 614 LEU cc_start: 0.8664 (tt) cc_final: 0.8409 (pp) REVERT: E 699 TYR cc_start: 0.7710 (t80) cc_final: 0.7500 (t80) REVERT: E 784 MET cc_start: 0.7336 (mmp) cc_final: 0.7007 (mtp) REVERT: F 287 LYS cc_start: 0.7754 (mmpt) cc_final: 0.7373 (mmtp) REVERT: F 359 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8400 (ttm110) REVERT: F 483 ASN cc_start: 0.7671 (p0) cc_final: 0.7286 (t0) REVERT: F 588 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8634 (mt-10) REVERT: F 621 MET cc_start: 0.8035 (ppp) cc_final: 0.7819 (ppp) REVERT: G 133 LYS cc_start: 0.8638 (tmtt) cc_final: 0.8155 (tttt) REVERT: G 218 LYS cc_start: 0.8767 (ptmt) cc_final: 0.8334 (ptmt) REVERT: G 387 SER cc_start: 0.8540 (p) cc_final: 0.8202 (t) REVERT: G 455 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7817 (Cg_exo) REVERT: G 548 ILE cc_start: 0.9172 (pt) cc_final: 0.8931 (pt) REVERT: I 29 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8634 (ttpp) outliers start: 33 outliers final: 12 residues processed: 614 average time/residue: 0.5402 time to fit residues: 500.8901 Evaluate side-chains 322 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 309 time to evaluate : 4.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 225 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 0.0370 chunk 325 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 336 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 204 optimal weight: 0.2980 chunk 250 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 overall best weight: 2.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 225 GLN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN B 193 HIS B 394 HIS ** D 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN E 432 GLN F 295 ASN F 394 HIS G 106 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN G 528 HIS ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 34819 Z= 0.342 Angle : 0.676 9.333 47111 Z= 0.328 Chirality : 0.045 0.236 5306 Planarity : 0.004 0.044 6138 Dihedral : 10.975 154.384 4957 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 2.31 % Allowed : 9.84 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.14 (0.13), residues: 4274 helix: 1.81 (0.12), residues: 2007 sheet: -0.17 (0.22), residues: 568 loop : -0.11 (0.16), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 252 HIS 0.031 0.001 HIS A 716 PHE 0.021 0.002 PHE G 381 TYR 0.023 0.002 TYR G 507 ARG 0.007 0.001 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 320 time to evaluate : 4.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8657 (mm-30) REVERT: A 194 TRP cc_start: 0.1739 (p90) cc_final: 0.0346 (t60) REVERT: A 229 MET cc_start: 0.8595 (mtt) cc_final: 0.8335 (mtt) REVERT: A 378 ASP cc_start: 0.8521 (t0) cc_final: 0.8196 (t0) REVERT: B 56 MET cc_start: 0.6886 (ptt) cc_final: 0.6214 (mpp) REVERT: B 62 PHE cc_start: 0.7045 (m-80) cc_final: 0.6713 (p90) REVERT: B 65 ASP cc_start: 0.5000 (OUTLIER) cc_final: 0.4114 (p0) REVERT: B 86 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: B 183 TYR cc_start: 0.7263 (p90) cc_final: 0.7028 (p90) REVERT: B 301 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 315 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8051 (mm-30) REVERT: B 483 ASN cc_start: 0.8543 (t0) cc_final: 0.8117 (p0) REVERT: B 557 LEU cc_start: 0.9233 (mt) cc_final: 0.9026 (mt) REVERT: B 560 MET cc_start: 0.7231 (mtt) cc_final: 0.6741 (tpt) REVERT: C 246 LYS cc_start: 0.9079 (mttt) cc_final: 0.8870 (ptmt) REVERT: C 317 ASP cc_start: 0.7957 (p0) cc_final: 0.7713 (t0) REVERT: C 342 MET cc_start: 0.8684 (tpp) cc_final: 0.8154 (mmm) REVERT: C 348 ARG cc_start: 0.8636 (mtt90) cc_final: 0.7539 (mmm160) REVERT: C 437 MET cc_start: 0.8430 (tpp) cc_final: 0.8160 (tpp) REVERT: C 570 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7050 (tpp80) REVERT: D 331 GLU cc_start: 0.8144 (mp0) cc_final: 0.7877 (mp0) REVERT: D 402 ASP cc_start: 0.8014 (m-30) cc_final: 0.7575 (p0) REVERT: E 288 MET cc_start: 0.6989 (mmm) cc_final: 0.6753 (mmm) REVERT: E 430 MET cc_start: 0.8147 (tpp) cc_final: 0.7798 (ttp) REVERT: E 500 LYS cc_start: 0.7061 (mttt) cc_final: 0.6763 (ptpt) REVERT: E 784 MET cc_start: 0.7475 (mmp) cc_final: 0.7141 (mtp) REVERT: F 359 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8251 (ttm110) REVERT: F 483 ASN cc_start: 0.7698 (p0) cc_final: 0.7283 (t0) REVERT: F 556 GLU cc_start: 0.8843 (mp0) cc_final: 0.8339 (mp0) REVERT: F 588 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8656 (mt-10) REVERT: G 126 ASP cc_start: 0.8438 (p0) cc_final: 0.8220 (p0) REVERT: G 422 MET cc_start: 0.8464 (mmm) cc_final: 0.8149 (mmm) REVERT: H 288 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7484 (mt-10) REVERT: I 18 GLU cc_start: 0.8296 (mp0) cc_final: 0.7925 (mp0) REVERT: I 29 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8693 (ttpp) outliers start: 85 outliers final: 51 residues processed: 381 average time/residue: 0.4651 time to fit residues: 285.4394 Evaluate side-chains 325 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 272 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 716 HIS Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 225 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 324 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 390 optimal weight: 2.9990 chunk 421 optimal weight: 9.9990 chunk 347 optimal weight: 10.0000 chunk 387 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS A 548 ASN A 670 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34819 Z= 0.204 Angle : 0.591 9.386 47111 Z= 0.282 Chirality : 0.042 0.148 5306 Planarity : 0.004 0.042 6138 Dihedral : 10.351 147.799 4952 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Rotamer: Outliers : 2.58 % Allowed : 11.22 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.24 (0.14), residues: 4274 helix: 1.83 (0.12), residues: 2010 sheet: -0.04 (0.22), residues: 570 loop : 0.01 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 252 HIS 0.016 0.001 HIS A 716 PHE 0.012 0.001 PHE G 260 TYR 0.026 0.001 TYR G 507 ARG 0.006 0.000 ARG F 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 306 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TRP cc_start: 0.1699 (p90) cc_final: 0.0568 (t60) REVERT: A 208 MET cc_start: 0.8763 (tmm) cc_final: 0.8062 (tmm) REVERT: A 266 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7343 (mmm160) REVERT: A 341 LEU cc_start: 0.9309 (mt) cc_final: 0.9100 (mt) REVERT: A 378 ASP cc_start: 0.8634 (t0) cc_final: 0.8386 (t0) REVERT: B 65 ASP cc_start: 0.5106 (OUTLIER) cc_final: 0.4243 (p0) REVERT: B 86 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: B 151 GLU cc_start: 0.7448 (mp0) cc_final: 0.5981 (tm-30) REVERT: B 183 TYR cc_start: 0.7392 (p90) cc_final: 0.7136 (p90) REVERT: B 301 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 315 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8132 (mm-30) REVERT: B 329 GLU cc_start: 0.6996 (tp30) cc_final: 0.6668 (tp30) REVERT: B 483 ASN cc_start: 0.8482 (t0) cc_final: 0.8141 (p0) REVERT: B 557 LEU cc_start: 0.9233 (mt) cc_final: 0.9012 (mt) REVERT: B 560 MET cc_start: 0.7268 (mtt) cc_final: 0.6750 (tpt) REVERT: C 246 LYS cc_start: 0.9094 (mttt) cc_final: 0.8852 (ptmt) REVERT: C 317 ASP cc_start: 0.7929 (p0) cc_final: 0.7646 (t0) REVERT: C 342 MET cc_start: 0.8618 (tpp) cc_final: 0.8117 (mmm) REVERT: C 348 ARG cc_start: 0.8623 (mtt90) cc_final: 0.7561 (mmm160) REVERT: C 570 ARG cc_start: 0.8350 (mmm160) cc_final: 0.6955 (tpp80) REVERT: D 330 VAL cc_start: 0.7911 (m) cc_final: 0.7704 (m) REVERT: D 331 GLU cc_start: 0.8105 (mp0) cc_final: 0.7864 (mp0) REVERT: D 402 ASP cc_start: 0.7966 (m-30) cc_final: 0.7616 (p0) REVERT: E 283 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7471 (mt-10) REVERT: E 430 MET cc_start: 0.8244 (tpp) cc_final: 0.7886 (ttp) REVERT: E 784 MET cc_start: 0.7456 (mmp) cc_final: 0.7131 (mtp) REVERT: F 323 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8232 (mtt180) REVERT: F 359 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8303 (ttm110) REVERT: F 364 ASP cc_start: 0.8595 (t0) cc_final: 0.8206 (t0) REVERT: F 483 ASN cc_start: 0.7715 (p0) cc_final: 0.7249 (t0) REVERT: F 556 GLU cc_start: 0.8777 (mp0) cc_final: 0.8330 (mp0) REVERT: F 588 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8671 (mt-10) REVERT: F 699 TYR cc_start: 0.8902 (t80) cc_final: 0.8685 (t80) REVERT: G 126 ASP cc_start: 0.8378 (p0) cc_final: 0.8126 (p0) REVERT: H 232 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8406 (p) REVERT: I 18 GLU cc_start: 0.8272 (mp0) cc_final: 0.7877 (mp0) REVERT: I 29 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8641 (ttpp) outliers start: 95 outliers final: 54 residues processed: 374 average time/residue: 0.4627 time to fit residues: 282.4338 Evaluate side-chains 338 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 280 time to evaluate : 4.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 716 HIS Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 220 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 3.9990 chunk 293 optimal weight: 0.2980 chunk 202 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 186 optimal weight: 0.0050 chunk 262 optimal weight: 0.0770 chunk 391 optimal weight: 0.4980 chunk 414 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 371 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.1950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 225 GLN B 548 ASN E 638 GLN F 432 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34819 Z= 0.140 Angle : 0.573 8.721 47111 Z= 0.269 Chirality : 0.041 0.153 5306 Planarity : 0.003 0.046 6138 Dihedral : 9.680 143.034 4946 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 2.36 % Allowed : 12.58 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.31 (0.14), residues: 4274 helix: 1.83 (0.12), residues: 2014 sheet: 0.08 (0.22), residues: 572 loop : 0.07 (0.17), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 561 HIS 0.016 0.001 HIS D 509 PHE 0.022 0.001 PHE D 628 TYR 0.025 0.001 TYR G 507 ARG 0.009 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 313 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TRP cc_start: 0.1909 (p90) cc_final: 0.1081 (t60) REVERT: A 208 MET cc_start: 0.8577 (tmm) cc_final: 0.7577 (tmm) REVERT: A 266 ARG cc_start: 0.8125 (mmm160) cc_final: 0.7220 (mmm160) REVERT: A 341 LEU cc_start: 0.9309 (mt) cc_final: 0.9099 (mt) REVERT: B 86 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8497 (pt0) REVERT: B 168 MET cc_start: 0.6175 (tpp) cc_final: 0.5940 (ttm) REVERT: B 183 TYR cc_start: 0.7459 (p90) cc_final: 0.7191 (p90) REVERT: B 301 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 315 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8313 (mm-30) REVERT: B 483 ASN cc_start: 0.8411 (t0) cc_final: 0.8058 (p0) REVERT: C 280 ASN cc_start: 0.7907 (t0) cc_final: 0.7694 (t0) REVERT: C 342 MET cc_start: 0.8459 (tpp) cc_final: 0.8006 (mmm) REVERT: C 348 ARG cc_start: 0.8617 (mtt90) cc_final: 0.7555 (mmm160) REVERT: C 570 ARG cc_start: 0.8275 (mmm160) cc_final: 0.6869 (tpp80) REVERT: C 571 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8539 (m-30) REVERT: D 223 MET cc_start: 0.9052 (tpp) cc_final: 0.7642 (mmm) REVERT: D 402 ASP cc_start: 0.7889 (m-30) cc_final: 0.7561 (p0) REVERT: E 208 MET cc_start: 0.7169 (tpt) cc_final: 0.6968 (mmm) REVERT: E 430 MET cc_start: 0.8223 (tpp) cc_final: 0.7866 (ttp) REVERT: E 784 MET cc_start: 0.7446 (mmp) cc_final: 0.7114 (mtp) REVERT: F 264 MET cc_start: 0.8753 (tpt) cc_final: 0.8530 (tpt) REVERT: F 323 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8325 (mtt180) REVERT: F 359 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8054 (tpp-160) REVERT: F 483 ASN cc_start: 0.7716 (p0) cc_final: 0.7242 (t0) REVERT: F 588 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8693 (mt-10) REVERT: F 699 TYR cc_start: 0.8955 (t80) cc_final: 0.8717 (t80) REVERT: G 112 ARG cc_start: 0.7681 (ttt180) cc_final: 0.7301 (ptm160) REVERT: G 126 ASP cc_start: 0.8379 (p0) cc_final: 0.8132 (p0) REVERT: G 422 MET cc_start: 0.8197 (mmm) cc_final: 0.7820 (mmm) REVERT: H 232 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8327 (p) REVERT: H 288 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7422 (mt-10) REVERT: I 29 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8607 (ttpp) outliers start: 87 outliers final: 44 residues processed: 376 average time/residue: 0.4382 time to fit residues: 273.4110 Evaluate side-chains 325 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 277 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 308 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 0.7980 chunk 372 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN E 638 GLN F 432 GLN G 170 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 260 ASN ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 34819 Z= 0.413 Angle : 0.695 8.743 47111 Z= 0.339 Chirality : 0.045 0.200 5306 Planarity : 0.004 0.048 6138 Dihedral : 9.580 137.794 4942 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.87 % Rotamer: Outliers : 3.23 % Allowed : 13.12 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4274 helix: 1.57 (0.12), residues: 1992 sheet: -0.12 (0.22), residues: 562 loop : -0.25 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 252 HIS 0.010 0.001 HIS A 716 PHE 0.026 0.002 PHE G 381 TYR 0.024 0.002 TYR G 189 ARG 0.007 0.001 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 276 time to evaluate : 3.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TRP cc_start: 0.1780 (p90) cc_final: 0.0794 (t60) REVERT: A 208 MET cc_start: 0.8568 (tmm) cc_final: 0.8356 (tmm) REVERT: B 151 GLU cc_start: 0.7430 (mp0) cc_final: 0.5921 (tm-30) REVERT: B 183 TYR cc_start: 0.7587 (p90) cc_final: 0.7279 (p90) REVERT: B 254 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7783 (p90) REVERT: B 301 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 315 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8354 (mm-30) REVERT: B 483 ASN cc_start: 0.8565 (t0) cc_final: 0.8106 (p0) REVERT: C 280 ASN cc_start: 0.8276 (t0) cc_final: 0.8062 (t0) REVERT: C 348 ARG cc_start: 0.8619 (mtt90) cc_final: 0.7594 (mmm160) REVERT: C 570 ARG cc_start: 0.8464 (mmm160) cc_final: 0.7171 (tpp80) REVERT: C 621 MET cc_start: 0.6722 (pmm) cc_final: 0.5971 (ptp) REVERT: C 762 MET cc_start: 0.5757 (tmm) cc_final: 0.5509 (ptt) REVERT: D 223 MET cc_start: 0.8976 (tpp) cc_final: 0.8202 (mmm) REVERT: D 285 MET cc_start: 0.8917 (tpp) cc_final: 0.8553 (tpp) REVERT: E 283 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7531 (mt-10) REVERT: E 430 MET cc_start: 0.8267 (tpp) cc_final: 0.7944 (ttp) REVERT: E 459 MET cc_start: 0.7930 (mmm) cc_final: 0.7723 (mmm) REVERT: E 500 LYS cc_start: 0.6686 (mttt) cc_final: 0.6375 (mttt) REVERT: E 784 MET cc_start: 0.7434 (mmp) cc_final: 0.7146 (mtp) REVERT: F 254 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7500 (p90) REVERT: F 264 MET cc_start: 0.8869 (tpt) cc_final: 0.8577 (tpt) REVERT: F 359 ARG cc_start: 0.8742 (tpp80) cc_final: 0.8123 (tpp-160) REVERT: F 483 ASN cc_start: 0.7735 (p0) cc_final: 0.7202 (t0) REVERT: F 588 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8715 (mt-10) REVERT: G 112 ARG cc_start: 0.7781 (ttt180) cc_final: 0.7509 (ptm160) REVERT: G 126 ASP cc_start: 0.8571 (p0) cc_final: 0.8266 (p0) REVERT: G 422 MET cc_start: 0.8641 (mmm) cc_final: 0.8219 (mmm) REVERT: H 232 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8467 (p) REVERT: H 288 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7503 (mt-10) REVERT: I 29 LYS cc_start: 0.8935 (ttpt) cc_final: 0.8517 (tttt) outliers start: 119 outliers final: 84 residues processed: 372 average time/residue: 0.4482 time to fit residues: 275.5622 Evaluate side-chains 352 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 265 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 716 HIS Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 460 ASP Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 9.9990 chunk 373 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 243 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 415 optimal weight: 0.7980 chunk 344 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN C 361 ASN C 668 ASN F 432 GLN G 577 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34819 Z= 0.184 Angle : 0.584 8.717 47111 Z= 0.279 Chirality : 0.042 0.208 5306 Planarity : 0.004 0.050 6138 Dihedral : 9.205 137.637 4942 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.44 % Rotamer: Outliers : 2.34 % Allowed : 14.67 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.07 (0.14), residues: 4274 helix: 1.70 (0.12), residues: 1995 sheet: 0.02 (0.23), residues: 562 loop : -0.15 (0.16), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 252 HIS 0.009 0.001 HIS A 716 PHE 0.013 0.001 PHE C 370 TYR 0.025 0.001 TYR G 507 ARG 0.004 0.000 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 280 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TRP cc_start: 0.2014 (p90) cc_final: 0.1018 (t60) REVERT: A 229 MET cc_start: 0.8563 (mtt) cc_final: 0.8315 (mtp) REVERT: B 60 GLU cc_start: 0.8403 (mp0) cc_final: 0.7854 (pp20) REVERT: B 151 GLU cc_start: 0.7454 (mp0) cc_final: 0.5846 (tm-30) REVERT: B 183 TYR cc_start: 0.7491 (p90) cc_final: 0.7168 (p90) REVERT: B 301 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 315 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8320 (mm-30) REVERT: B 483 ASN cc_start: 0.8506 (t0) cc_final: 0.8103 (p0) REVERT: C 280 ASN cc_start: 0.8206 (t0) cc_final: 0.8002 (t0) REVERT: C 342 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7250 (mpp) REVERT: C 348 ARG cc_start: 0.8625 (mtt90) cc_final: 0.7571 (mmm160) REVERT: C 570 ARG cc_start: 0.8381 (mmm160) cc_final: 0.7044 (tpp80) REVERT: C 621 MET cc_start: 0.6690 (pmm) cc_final: 0.6095 (ptp) REVERT: C 762 MET cc_start: 0.5715 (tmm) cc_final: 0.5458 (ptt) REVERT: D 264 MET cc_start: 0.9046 (tpp) cc_final: 0.8657 (tpp) REVERT: D 315 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8355 (mm-30) REVERT: D 402 ASP cc_start: 0.7990 (m-30) cc_final: 0.7572 (p0) REVERT: E 263 LEU cc_start: 0.8421 (tt) cc_final: 0.7963 (mm) REVERT: E 342 MET cc_start: 0.9087 (mmm) cc_final: 0.8671 (mmm) REVERT: E 430 MET cc_start: 0.8237 (tpp) cc_final: 0.7920 (ttp) REVERT: E 459 MET cc_start: 0.7932 (mmm) cc_final: 0.7638 (mmm) REVERT: E 500 LYS cc_start: 0.6689 (mttt) cc_final: 0.6394 (mttt) REVERT: E 784 MET cc_start: 0.7436 (mmp) cc_final: 0.7106 (mtp) REVERT: F 264 MET cc_start: 0.8898 (tpt) cc_final: 0.8647 (tpt) REVERT: F 359 ARG cc_start: 0.8738 (tpp80) cc_final: 0.8041 (tpp-160) REVERT: F 483 ASN cc_start: 0.7716 (p0) cc_final: 0.7198 (t0) REVERT: F 588 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8728 (mt-10) REVERT: G 112 ARG cc_start: 0.7633 (ttt180) cc_final: 0.7337 (ptm160) REVERT: G 422 MET cc_start: 0.8509 (mmm) cc_final: 0.8214 (mmm) REVERT: H 232 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8398 (p) REVERT: H 288 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7672 (mt-10) REVERT: I 29 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8647 (ttpp) outliers start: 86 outliers final: 60 residues processed: 343 average time/residue: 0.4387 time to fit residues: 252.2618 Evaluate side-chains 329 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 267 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 220 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 349 optimal weight: 0.9980 chunk 231 optimal weight: 0.7980 chunk 413 optimal weight: 2.9990 chunk 258 optimal weight: 0.6980 chunk 252 optimal weight: 0.0270 chunk 190 optimal weight: 0.0060 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN E 638 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34819 Z= 0.143 Angle : 0.572 12.090 47111 Z= 0.269 Chirality : 0.041 0.272 5306 Planarity : 0.003 0.041 6138 Dihedral : 8.925 143.456 4942 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 2.23 % Allowed : 15.05 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.17 (0.14), residues: 4274 helix: 1.75 (0.12), residues: 1992 sheet: 0.13 (0.23), residues: 562 loop : -0.08 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 252 HIS 0.008 0.001 HIS A 716 PHE 0.016 0.001 PHE B 144 TYR 0.024 0.001 TYR D 254 ARG 0.010 0.000 ARG D 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 288 time to evaluate : 4.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6949 (ptp) cc_final: 0.5195 (mtt) REVERT: A 161 HIS cc_start: 0.7621 (m-70) cc_final: 0.7402 (m-70) REVERT: A 194 TRP cc_start: 0.1978 (p90) cc_final: 0.1018 (t60) REVERT: A 266 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7399 (mmm160) REVERT: A 398 MET cc_start: 0.8420 (mtp) cc_final: 0.7933 (mtm) REVERT: A 437 MET cc_start: 0.8279 (ppp) cc_final: 0.8010 (ppp) REVERT: B 60 GLU cc_start: 0.8377 (mp0) cc_final: 0.7707 (pp20) REVERT: B 151 GLU cc_start: 0.7344 (mp0) cc_final: 0.5773 (tm-30) REVERT: B 168 MET cc_start: 0.6001 (tpp) cc_final: 0.5751 (tpp) REVERT: B 183 TYR cc_start: 0.7509 (p90) cc_final: 0.7175 (p90) REVERT: B 301 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 315 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8321 (mm-30) REVERT: B 483 ASN cc_start: 0.8425 (t0) cc_final: 0.8069 (p0) REVERT: C 280 ASN cc_start: 0.8108 (t0) cc_final: 0.7904 (t0) REVERT: C 342 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8121 (mpp) REVERT: C 348 ARG cc_start: 0.8631 (mtt90) cc_final: 0.7569 (mmm160) REVERT: C 570 ARG cc_start: 0.8356 (mmm160) cc_final: 0.7005 (tpp80) REVERT: C 621 MET cc_start: 0.6695 (pmm) cc_final: 0.6008 (ptp) REVERT: C 762 MET cc_start: 0.5711 (tmm) cc_final: 0.5465 (ptt) REVERT: D 223 MET cc_start: 0.8947 (tpt) cc_final: 0.8567 (mmm) REVERT: D 402 ASP cc_start: 0.7965 (m-30) cc_final: 0.7537 (p0) REVERT: E 263 LEU cc_start: 0.8387 (tt) cc_final: 0.7938 (mm) REVERT: E 342 MET cc_start: 0.9105 (mmm) cc_final: 0.8758 (mmm) REVERT: E 430 MET cc_start: 0.8222 (tpp) cc_final: 0.7868 (ttp) REVERT: E 500 LYS cc_start: 0.6584 (mttt) cc_final: 0.6334 (mttt) REVERT: E 626 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7034 (t0) REVERT: E 784 MET cc_start: 0.7434 (mmp) cc_final: 0.7107 (mtp) REVERT: F 264 MET cc_start: 0.8975 (tpt) cc_final: 0.8720 (tpp) REVERT: F 359 ARG cc_start: 0.8718 (tpp80) cc_final: 0.8023 (tpp-160) REVERT: F 483 ASN cc_start: 0.7700 (p0) cc_final: 0.7185 (t0) REVERT: F 588 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8730 (mt-10) REVERT: G 112 ARG cc_start: 0.7671 (ttt180) cc_final: 0.7308 (ptm160) REVERT: G 422 MET cc_start: 0.8490 (mmm) cc_final: 0.8218 (mmm) REVERT: H 232 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8400 (p) REVERT: H 288 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7633 (mt-10) REVERT: I 29 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8639 (ttpp) outliers start: 82 outliers final: 63 residues processed: 346 average time/residue: 0.4409 time to fit residues: 254.0312 Evaluate side-chains 339 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 273 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 220 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 325 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS C 612 ASN C 668 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34819 Z= 0.235 Angle : 0.601 10.443 47111 Z= 0.287 Chirality : 0.042 0.269 5306 Planarity : 0.004 0.043 6138 Dihedral : 8.873 146.256 4942 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 2.42 % Allowed : 15.49 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.10 (0.14), residues: 4274 helix: 1.74 (0.12), residues: 1996 sheet: 0.08 (0.23), residues: 561 loop : -0.16 (0.16), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 561 HIS 0.007 0.001 HIS A 716 PHE 0.017 0.001 PHE B 628 TYR 0.033 0.001 TYR G 189 ARG 0.010 0.000 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 275 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6960 (ptp) cc_final: 0.5273 (mtt) REVERT: A 161 HIS cc_start: 0.7693 (m-70) cc_final: 0.7483 (m-70) REVERT: A 194 TRP cc_start: 0.1997 (p90) cc_final: 0.1019 (t60) REVERT: A 266 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7435 (mmm160) REVERT: A 398 MET cc_start: 0.8462 (mtp) cc_final: 0.7935 (mtm) REVERT: A 566 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7487 (pp20) REVERT: B 168 MET cc_start: 0.6194 (tpp) cc_final: 0.5991 (tpp) REVERT: B 183 TYR cc_start: 0.7524 (p90) cc_final: 0.7191 (p90) REVERT: B 301 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 315 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8378 (mm-30) REVERT: B 483 ASN cc_start: 0.8447 (t0) cc_final: 0.8040 (p0) REVERT: C 280 ASN cc_start: 0.8283 (t0) cc_final: 0.8078 (t0) REVERT: C 342 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8174 (mpp) REVERT: C 348 ARG cc_start: 0.8650 (mtt90) cc_final: 0.7602 (mmm160) REVERT: C 570 ARG cc_start: 0.8396 (mmm160) cc_final: 0.7078 (tpp80) REVERT: C 621 MET cc_start: 0.6752 (pmm) cc_final: 0.6180 (ptp) REVERT: C 762 MET cc_start: 0.5626 (tmm) cc_final: 0.5377 (ptt) REVERT: D 223 MET cc_start: 0.8957 (tpt) cc_final: 0.8561 (mmm) REVERT: E 263 LEU cc_start: 0.8507 (tt) cc_final: 0.8026 (mm) REVERT: E 283 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7640 (mt-10) REVERT: E 342 MET cc_start: 0.9156 (mmm) cc_final: 0.8829 (mmm) REVERT: E 430 MET cc_start: 0.8244 (tpp) cc_final: 0.7931 (ttp) REVERT: E 459 MET cc_start: 0.7948 (mmm) cc_final: 0.7625 (mmm) REVERT: E 626 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7191 (t0) REVERT: E 784 MET cc_start: 0.7407 (mmp) cc_final: 0.7083 (mtp) REVERT: F 264 MET cc_start: 0.9025 (tpt) cc_final: 0.8734 (tpt) REVERT: F 342 MET cc_start: 0.8911 (tpt) cc_final: 0.8504 (tpt) REVERT: F 345 MET cc_start: 0.7444 (mmm) cc_final: 0.7213 (mmm) REVERT: F 359 ARG cc_start: 0.8725 (tpp80) cc_final: 0.8020 (tpp-160) REVERT: F 483 ASN cc_start: 0.7666 (p0) cc_final: 0.7185 (t0) REVERT: F 513 TYR cc_start: 0.8389 (m-80) cc_final: 0.7870 (m-80) REVERT: F 588 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8736 (mt-10) REVERT: G 112 ARG cc_start: 0.7650 (ttt180) cc_final: 0.7321 (ptm160) REVERT: G 542 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7759 (p0) REVERT: H 232 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8468 (p) REVERT: H 288 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7692 (mt-10) REVERT: I 29 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8644 (ttpp) outliers start: 89 outliers final: 71 residues processed: 344 average time/residue: 0.4299 time to fit residues: 247.1220 Evaluate side-chains 342 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 266 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain G residue 542 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 220 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 0.8980 chunk 396 optimal weight: 0.0170 chunk 361 optimal weight: 3.9990 chunk 385 optimal weight: 0.9980 chunk 231 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 348 optimal weight: 1.9990 chunk 364 optimal weight: 0.2980 chunk 383 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS C 668 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34819 Z= 0.147 Angle : 0.589 11.597 47111 Z= 0.278 Chirality : 0.041 0.274 5306 Planarity : 0.003 0.042 6138 Dihedral : 8.643 146.627 4940 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 2.09 % Allowed : 15.95 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.19 (0.14), residues: 4274 helix: 1.79 (0.12), residues: 1986 sheet: 0.18 (0.23), residues: 564 loop : -0.09 (0.16), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 252 HIS 0.007 0.001 HIS A 716 PHE 0.028 0.001 PHE B 628 TYR 0.024 0.001 TYR G 189 ARG 0.014 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 281 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7885 (pmm) cc_final: 0.6227 (tpt) REVERT: A 161 HIS cc_start: 0.7636 (m-70) cc_final: 0.7421 (m-70) REVERT: A 183 TYR cc_start: 0.4172 (p90) cc_final: 0.3941 (p90) REVERT: A 194 TRP cc_start: 0.1921 (p90) cc_final: 0.1078 (t60) REVERT: A 266 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7344 (mmm160) REVERT: A 285 MET cc_start: 0.8491 (tpp) cc_final: 0.7962 (mpp) REVERT: A 341 LEU cc_start: 0.9376 (mt) cc_final: 0.9165 (tp) REVERT: A 350 ASN cc_start: 0.7503 (m-40) cc_final: 0.7258 (m-40) REVERT: A 398 MET cc_start: 0.8376 (mtp) cc_final: 0.7838 (mtm) REVERT: A 566 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: B 151 GLU cc_start: 0.7279 (mp0) cc_final: 0.6327 (tm-30) REVERT: B 183 TYR cc_start: 0.7469 (p90) cc_final: 0.7124 (p90) REVERT: B 301 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 315 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8330 (mm-30) REVERT: B 483 ASN cc_start: 0.8416 (t0) cc_final: 0.8051 (p0) REVERT: C 342 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8196 (mpp) REVERT: C 348 ARG cc_start: 0.8640 (mtt90) cc_final: 0.7559 (mmm160) REVERT: C 570 ARG cc_start: 0.8390 (mmm160) cc_final: 0.7028 (tpp80) REVERT: C 621 MET cc_start: 0.6724 (pmm) cc_final: 0.6094 (ptp) REVERT: C 762 MET cc_start: 0.5593 (tmm) cc_final: 0.5329 (ptt) REVERT: D 402 ASP cc_start: 0.8018 (m-30) cc_final: 0.7584 (p0) REVERT: E 263 LEU cc_start: 0.8416 (tt) cc_final: 0.7964 (mm) REVERT: E 283 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7600 (mt-10) REVERT: E 342 MET cc_start: 0.9154 (mmm) cc_final: 0.8890 (mmm) REVERT: E 430 MET cc_start: 0.8214 (tpp) cc_final: 0.7895 (ttp) REVERT: E 626 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7019 (t0) REVERT: E 784 MET cc_start: 0.7432 (mmp) cc_final: 0.7102 (mtp) REVERT: F 264 MET cc_start: 0.9009 (tpt) cc_final: 0.8749 (tpt) REVERT: F 342 MET cc_start: 0.8889 (tpt) cc_final: 0.8554 (tpt) REVERT: F 345 MET cc_start: 0.7411 (mmm) cc_final: 0.7123 (mmm) REVERT: F 359 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8031 (tpp-160) REVERT: F 483 ASN cc_start: 0.7631 (p0) cc_final: 0.7167 (t0) REVERT: F 588 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8774 (mt-10) REVERT: G 112 ARG cc_start: 0.7663 (ttt180) cc_final: 0.7282 (ptm160) REVERT: G 542 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7791 (p0) REVERT: H 232 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8493 (p) REVERT: H 288 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7671 (mt-10) REVERT: I 29 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8614 (ttpp) outliers start: 77 outliers final: 56 residues processed: 337 average time/residue: 0.4661 time to fit residues: 264.2140 Evaluate side-chains 330 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 269 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain G residue 542 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 220 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 4.9990 chunk 407 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 427 optimal weight: 6.9990 chunk 393 optimal weight: 4.9990 chunk 340 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 262 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34819 Z= 0.246 Angle : 0.622 11.614 47111 Z= 0.296 Chirality : 0.042 0.262 5306 Planarity : 0.004 0.047 6138 Dihedral : 8.585 146.591 4940 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 1.88 % Allowed : 16.33 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.13 (0.14), residues: 4274 helix: 1.76 (0.12), residues: 1986 sheet: 0.08 (0.23), residues: 566 loop : -0.14 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 252 HIS 0.006 0.001 HIS A 716 PHE 0.014 0.001 PHE G 260 TYR 0.039 0.001 TYR G 189 ARG 0.009 0.000 ARG C 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 264 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7973 (pmm) cc_final: 0.6199 (tpt) REVERT: A 56 MET cc_start: 0.6951 (ptp) cc_final: 0.5305 (mtt) REVERT: A 183 TYR cc_start: 0.4110 (p90) cc_final: 0.3892 (p90) REVERT: A 194 TRP cc_start: 0.1922 (p90) cc_final: 0.1085 (t60) REVERT: A 266 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7448 (mmm160) REVERT: A 350 ASN cc_start: 0.7580 (m-40) cc_final: 0.7322 (m-40) REVERT: A 398 MET cc_start: 0.8437 (mtp) cc_final: 0.7888 (mtm) REVERT: A 566 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7247 (pp20) REVERT: B 151 GLU cc_start: 0.7246 (mp0) cc_final: 0.6074 (tm-30) REVERT: B 183 TYR cc_start: 0.7513 (p90) cc_final: 0.7182 (p90) REVERT: B 301 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 315 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8382 (mm-30) REVERT: B 483 ASN cc_start: 0.8447 (t0) cc_final: 0.8036 (p0) REVERT: C 342 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8301 (mpp) REVERT: C 348 ARG cc_start: 0.8652 (mtt90) cc_final: 0.7582 (mmm160) REVERT: C 570 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7043 (tpp80) REVERT: C 588 GLU cc_start: 0.7390 (tt0) cc_final: 0.7128 (tt0) REVERT: C 621 MET cc_start: 0.6895 (pmm) cc_final: 0.6338 (ptp) REVERT: C 762 MET cc_start: 0.5465 (tmm) cc_final: 0.5187 (ptt) REVERT: D 342 MET cc_start: 0.8508 (tpp) cc_final: 0.8185 (mmm) REVERT: E 263 LEU cc_start: 0.8514 (tt) cc_final: 0.8035 (mm) REVERT: E 283 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7646 (mt-10) REVERT: E 342 MET cc_start: 0.9282 (mmm) cc_final: 0.8984 (mmm) REVERT: E 430 MET cc_start: 0.8242 (tpp) cc_final: 0.7937 (ttp) REVERT: E 626 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7186 (t0) REVERT: E 784 MET cc_start: 0.7407 (mmp) cc_final: 0.7082 (mtp) REVERT: F 342 MET cc_start: 0.8923 (tpt) cc_final: 0.8525 (tpt) REVERT: F 345 MET cc_start: 0.7359 (mmm) cc_final: 0.7158 (mmm) REVERT: F 359 ARG cc_start: 0.8727 (tpp80) cc_final: 0.8406 (ttm110) REVERT: F 483 ASN cc_start: 0.7629 (p0) cc_final: 0.7146 (t0) REVERT: F 513 TYR cc_start: 0.8395 (m-80) cc_final: 0.7885 (m-80) REVERT: F 587 ASP cc_start: 0.8724 (t0) cc_final: 0.8328 (m-30) REVERT: F 588 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8780 (mt-10) REVERT: G 112 ARG cc_start: 0.7705 (ttt180) cc_final: 0.7346 (ptm160) REVERT: G 542 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7830 (p0) REVERT: H 288 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7718 (mt-10) REVERT: I 29 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8635 (ttpp) outliers start: 69 outliers final: 59 residues processed: 316 average time/residue: 0.4510 time to fit residues: 237.1006 Evaluate side-chains 324 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 261 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain G residue 542 ASP Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 220 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 1.9990 chunk 362 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 313 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 340 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 350 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.115503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085709 restraints weight = 109282.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085679 restraints weight = 61421.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086418 restraints weight = 44537.702| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34819 Z= 0.150 Angle : 0.591 11.257 47111 Z= 0.279 Chirality : 0.041 0.260 5306 Planarity : 0.003 0.045 6138 Dihedral : 8.414 144.740 4940 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 1.71 % Allowed : 16.66 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.19 (0.14), residues: 4274 helix: 1.80 (0.12), residues: 1989 sheet: 0.15 (0.23), residues: 574 loop : -0.10 (0.16), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 252 HIS 0.007 0.001 HIS A 716 PHE 0.014 0.001 PHE B 62 TYR 0.028 0.001 TYR G 189 ARG 0.010 0.000 ARG C 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6410.31 seconds wall clock time: 117 minutes 30.50 seconds (7050.50 seconds total)