Starting phenix.real_space_refine on Thu Feb 22 11:28:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8das_27274/02_2024/8das_27274_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8das_27274/02_2024/8das_27274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8das_27274/02_2024/8das_27274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8das_27274/02_2024/8das_27274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8das_27274/02_2024/8das_27274_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8das_27274/02_2024/8das_27274_updated.pdb" } resolution = 3.5 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= -0.016 sd= 1.079 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 21316 2.51 5 N 5920 2.21 5 O 6636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34059 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5560 Classifications: {'peptide': 712} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4385 Classifications: {'peptide': 564} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 534} Chain breaks: 5 Chain: "C" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5590 Classifications: {'peptide': 716} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 678} Chain breaks: 2 Chain: "D" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4365 Classifications: {'peptide': 561} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 531} Chain breaks: 4 Chain: "E" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4174 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 509} Chain breaks: 2 Chain: "F" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4190 Classifications: {'peptide': 541} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 511} Chain breaks: 2 Chain: "G" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3815 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "H" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain breaks: 1 Chain: "J" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 581 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28517 SG CYS G 137 42.490 46.648 95.636 1.00 75.98 S ATOM 28577 SG CYS G 145 46.079 47.436 95.068 1.00 61.42 S ATOM 28604 SG CYS G 148 44.717 46.971 98.444 1.00 62.85 S ATOM 29074 SG CYS G 204 71.751 88.637 114.245 1.00 85.09 S ATOM 29172 SG CYS G 216 72.055 90.528 111.078 1.00 68.03 S ATOM 29193 SG CYS G 219 69.351 91.363 113.359 1.00 67.48 S Time building chain proxies: 17.86, per 1000 atoms: 0.52 Number of scatterers: 34059 At special positions: 0 Unit cell: (146.832, 167.048, 192.584, 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 6636 8.00 N 5920 7.00 C 21316 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.45 Conformation dependent library (CDL) restraints added in 6.1 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 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 203 helices and 24 sheets defined 45.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.38 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 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 140 through 149 removed outlier: 4.086A 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 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.508A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 329 through 345 removed outlier: 4.147A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 439 removed outlier: 4.396A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.109A 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 545 removed outlier: 3.746A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 569 through 578 Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 641 through 644 Processing helix chain 'A' and resid 660 through 673 removed outlier: 4.954A pdb=" N LYS A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 689 Processing helix chain 'A' and resid 694 through 718 Processing helix chain 'A' and resid 755 through 763 Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'B' and resid 97 through 102 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: 4.203A 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 removed outlier: 3.666A pdb=" N ILE B 243 " --> pdb=" O PHE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.849A pdb=" N ASN B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.588A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.547A pdb=" N LYS B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 Processing helix chain 'B' and resid 418 through 439 removed outlier: 4.455A pdb=" N ASP B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 452 No H-bonds generated for 'chain 'B' and resid 449 through 452' 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: 4.583A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Proline residue: B 506 - end of helix Processing helix chain 'B' and resid 510 through 516 Processing helix chain 'B' and resid 534 through 544 Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 569 through 578 Processing helix chain 'B' and resid 589 through 592 No H-bonds generated for 'chain 'B' and resid 589 through 592' Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 641 through 644 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 683 through 689 Processing helix chain 'B' and resid 694 through 718 Processing helix chain 'B' and resid 755 through 764 removed outlier: 3.809A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 788 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 96 through 102 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 146 through 149 No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 220 through 235 removed outlier: 4.487A pdb=" N LEU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 237 through 243 removed outlier: 3.556A pdb=" N ILE C 243 " --> pdb=" O PHE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 272 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 292 through 306 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 329 through 344 removed outlier: 3.819A pdb=" N VAL C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.613A 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: 4.583A pdb=" N ASP C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 6.000A 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 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 493 through 508 removed outlier: 4.804A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 534 through 544 Processing helix chain 'C' and resid 554 through 562 Processing helix chain 'C' and resid 569 through 578 Processing helix chain 'C' and resid 589 through 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 641 through 644 Processing helix chain 'C' and resid 660 through 670 Processing helix chain 'C' and resid 683 through 689 Processing helix chain 'C' and resid 694 through 718 Processing helix chain 'C' and resid 755 through 763 Processing helix chain 'C' and resid 771 through 788 Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 202 through 205 No H-bonds generated for 'chain 'D' and resid 202 through 205' Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 220 through 235 removed outlier: 4.130A pdb=" N LEU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 237 through 243 Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 329 through 345 Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 384 through 396 removed outlier: 3.745A pdb=" N LYS D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 418 through 439 removed outlier: 4.521A pdb=" N ASP D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.753A pdb=" N SER D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) 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 493 through 508 removed outlier: 4.470A pdb=" N TYR D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Proline residue: D 506 - end of helix Processing helix chain 'D' and resid 510 through 516 Processing helix chain 'D' and resid 534 through 544 Processing helix chain 'D' and resid 554 through 562 Processing helix chain 'D' and resid 569 through 578 Processing helix chain 'D' and resid 589 through 592 No H-bonds generated for 'chain 'D' and resid 589 through 592' Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 641 through 644 Processing helix chain 'D' and resid 660 through 670 Processing helix chain 'D' and resid 683 through 689 Processing helix chain 'D' and resid 694 through 718 Processing helix chain 'D' and resid 755 through 763 Processing helix chain 'D' and resid 771 through 786 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 220 through 235 removed outlier: 4.119A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 261 through 272 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 292 through 305 Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 331 through 345 removed outlier: 4.222A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 367 No H-bonds generated for 'chain 'E' and resid 365 through 367' Processing helix chain 'E' and resid 384 through 396 removed outlier: 3.582A pdb=" N LYS E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 Processing helix chain 'E' and resid 418 through 438 removed outlier: 4.228A pdb=" N ASP E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 459 through 468 Processing helix chain 'E' and resid 473 through 475 No H-bonds generated for 'chain 'E' and resid 473 through 475' Processing helix chain 'E' and resid 493 through 508 removed outlier: 4.270A pdb=" N TYR E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) Proline residue: E 506 - end of helix Processing helix chain 'E' and resid 510 through 516 Processing helix chain 'E' and resid 534 through 544 Processing helix chain 'E' and resid 554 through 561 Processing helix chain 'E' and resid 569 through 578 Processing helix chain 'E' and resid 589 through 592 No H-bonds generated for 'chain 'E' and resid 589 through 592' Processing helix chain 'E' and resid 609 through 620 Processing helix chain 'E' and resid 641 through 644 Processing helix chain 'E' and resid 660 through 673 removed outlier: 4.728A pdb=" N LYS E 673 " --> pdb=" O ALA E 669 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 689 Processing helix chain 'E' and resid 694 through 718 Processing helix chain 'E' and resid 755 through 764 Processing helix chain 'E' and resid 771 through 786 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 220 through 235 removed outlier: 4.624A 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 305 Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 329 through 347 removed outlier: 4.080A pdb=" N LYS F 346 " --> pdb=" O MET F 342 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 367 No H-bonds generated for 'chain 'F' and resid 365 through 367' Processing helix chain 'F' and resid 384 through 394 Processing helix chain 'F' and resid 406 through 412 Processing helix chain 'F' and resid 418 through 439 removed outlier: 4.387A pdb=" N ASP F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 459 through 467 Processing helix chain 'F' and resid 473 through 475 No H-bonds generated for 'chain 'F' and resid 473 through 475' Processing helix chain 'F' and resid 493 through 508 removed outlier: 4.157A 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 591 No H-bonds generated for 'chain 'F' and resid 589 through 591' Processing helix chain 'F' and resid 609 through 619 Processing helix chain 'F' and resid 641 through 644 Processing helix chain 'F' and resid 660 through 671 Processing helix chain 'F' and resid 683 through 687 Processing helix chain 'F' and resid 694 through 718 Processing helix chain 'F' and resid 755 through 764 removed outlier: 3.939A pdb=" N THR F 764 " --> pdb=" O GLU F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 788 Processing helix chain 'G' and resid 117 through 124 Processing helix chain 'G' and resid 156 through 162 Processing helix chain 'G' and resid 169 through 179 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 243 through 255 removed outlier: 3.651A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 317 removed outlier: 3.818A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 364 Processing helix chain 'G' and resid 403 through 410 removed outlier: 3.869A pdb=" N THR G 410 " --> pdb=" O GLU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 462 Processing helix chain 'G' and resid 501 through 508 Processing helix chain 'G' and resid 510 through 514 removed outlier: 3.570A pdb=" N SER G 514 " --> pdb=" O ASN G 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 510 through 514' Processing helix chain 'G' and resid 517 through 522 Processing helix chain 'G' and resid 527 through 536 Processing helix chain 'G' and resid 541 through 551 Processing helix chain 'G' and resid 557 through 565 Processing helix chain 'G' and resid 567 through 578 Processing helix chain 'H' and resid 244 through 252 Processing 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 sheet with id= A, first strand: chain 'A' and resid 91 through 94 removed outlier: 7.999A pdb=" N CYS A 92 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU A 37 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 94 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP A 39 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 36 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 110 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 119 through 121 Processing sheet with id= C, first strand: chain 'A' and resid 191 through 193 removed outlier: 7.199A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.708A pdb=" N ARG A 375 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL A 251 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 353 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N MET A 253 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA A 355 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLY A 255 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR A 357 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 309 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A 354 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 311 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA A 356 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE A 313 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 651 through 654 removed outlier: 4.344A pdb=" N GLN A 651 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 524 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 629 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE A 526 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY A 631 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 582 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 630 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 584 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA A 632 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 586 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 375 through 379 removed outlier: 8.878A pdb=" N VAL B 251 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 353 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N MET B 253 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA B 355 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N GLY B 255 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 651 through 655 removed outlier: 4.338A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL B 524 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 629 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 526 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY B 631 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N GLY B 528 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR B 633 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR B 582 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 630 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 584 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA B 632 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 586 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= I, first strand: chain 'C' and resid 177 through 179 removed outlier: 6.347A pdb=" N ILE C 191 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.801A pdb=" N ARG C 154 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 161 through 166 removed outlier: 3.639A pdb=" N PHE C 162 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 376 through 379 removed outlier: 8.319A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE C 379 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR C 254 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL C 251 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 353 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET C 253 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 355 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N GLY C 255 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR C 357 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 651 through 654 removed outlier: 6.945A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN C 548 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N PHE C 585 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 550 " --> pdb=" O PHE C 585 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 375 through 379 removed outlier: 3.958A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL D 251 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 353 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET D 253 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA D 355 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY D 255 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR D 357 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 652 through 654 removed outlier: 8.425A pdb=" N ILE D 653 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU D 525 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N VAL D 524 " --> pdb=" O VAL D 627 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL D 629 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE D 526 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY D 631 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR D 582 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE D 630 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL D 584 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA D 632 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU D 586 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 375 through 379 removed outlier: 3.810A pdb=" N ARG E 375 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL E 353 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N MET E 253 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA E 355 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLY E 255 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR E 357 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 652 through 655 removed outlier: 8.558A pdb=" N ILE E 653 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU E 525 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL E 655 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR E 527 " --> pdb=" O VAL E 655 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL E 524 " --> pdb=" O VAL E 627 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL E 629 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE E 526 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY E 631 " --> pdb=" O PHE E 526 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N GLY E 528 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 375 through 379 removed outlier: 3.695A pdb=" N ARG F 375 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N VAL F 251 " --> pdb=" O VAL F 351 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL F 353 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET F 253 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA F 355 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY F 255 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR F 357 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 651 through 655 removed outlier: 3.591A pdb=" N GLY F 528 " --> pdb=" O THR F 633 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN F 548 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE F 585 " --> pdb=" O ASN F 548 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE F 550 " --> pdb=" O PHE F 585 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 224 through 226 removed outlier: 3.574A pdb=" N GLU G 451 " --> pdb=" O TYR G 439 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE G 447 " --> pdb=" O ASN G 443 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 467 through 470 removed outlier: 3.701A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL G 382 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N PHE G 326 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS G 384 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 422 through 424 removed outlier: 3.720A pdb=" N PHE G 457 " --> pdb=" O ALA G 423 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 112 through 116 removed outlier: 6.185A pdb=" N SER J 165 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LYS J 106 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU J 167 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 212 through 216 removed outlier: 5.903A pdb=" N SER K 265 " --> pdb=" O PHE K 204 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LYS K 206 " --> pdb=" O SER K 265 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU K 267 " --> pdb=" O LYS K 206 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU K 243 " --> pdb=" O LEU K 250 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE K 245 " --> pdb=" O LYS K 248 " (cutoff:3.500A) 1233 hydrogen bonds defined for protein. 3627 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: 11.67 Time building geometry restraints manager: 15.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11534 1.34 - 1.46: 6574 1.46 - 1.58: 16196 1.58 - 1.69: 46 1.69 - 1.81: 288 Bond restraints: 34638 Sorted by residual: bond pdb=" C4 ADP F 902 " pdb=" C5 ADP F 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+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 3.03e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5 ADP C 901 " pdb=" C6 ADP C 901 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 34633 not shown) Histogram of bond angle deviations from ideal: 99.17 - 107.32: 1398 107.32 - 115.47: 21218 115.47 - 123.62: 23483 123.62 - 131.77: 725 131.77 - 139.92: 46 Bond angle restraints: 46870 Sorted by residual: angle pdb=" N GLY G 323 " pdb=" CA GLY G 323 " pdb=" C GLY G 323 " ideal model delta sigma weight residual 110.96 115.83 -4.87 1.19e+00 7.06e-01 1.68e+01 angle pdb=" C1' ADP E 902 " pdb=" C2' ADP E 902 " pdb=" C3' ADP E 902 " ideal model delta sigma weight residual 111.00 100.28 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N ALA B 23 " pdb=" CA ALA B 23 " pdb=" C ALA B 23 " ideal model delta sigma weight residual 111.28 107.58 3.70 1.09e+00 8.42e-01 1.15e+01 angle pdb=" N ILE B 26 " pdb=" CA ILE B 26 " pdb=" C ILE B 26 " ideal model delta sigma weight residual 112.12 109.27 2.85 8.40e-01 1.42e+00 1.15e+01 angle pdb=" PA ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sigma weight residual 120.50 130.32 -9.82 3.00e+00 1.11e-01 1.07e+01 ... (remaining 46865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 21002 28.56 - 57.11: 368 57.11 - 85.67: 40 85.67 - 114.22: 6 114.22 - 142.78: 9 Dihedral angle restraints: 21425 sinusoidal: 8954 harmonic: 12471 Sorted by residual: dihedral pdb=" C2' ADP C 901 " pdb=" C1' ADP C 901 " pdb=" N9 ADP C 901 " pdb=" C4 ADP C 901 " ideal model delta sinusoidal sigma weight residual 91.55 -125.68 -142.78 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C2' ADP A 902 " pdb=" C1' ADP A 902 " pdb=" N9 ADP A 902 " pdb=" C4 ADP A 902 " ideal model delta sinusoidal sigma weight residual 91.55 -136.31 -132.15 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C4' ADP E 902 " pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " ideal model delta sinusoidal sigma weight residual 180.00 49.18 130.82 1 2.00e+01 2.50e-03 3.97e+01 ... (remaining 21422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4718 0.068 - 0.135: 522 0.135 - 0.203: 13 0.203 - 0.270: 5 0.270 - 0.338: 11 Chirality restraints: 5269 Sorted by residual: chirality pdb=" CA ASN G 510 " pdb=" N ASN G 510 " pdb=" C ASN G 510 " pdb=" CB ASN G 510 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C2' ATP A 901 " pdb=" C1' ATP A 901 " pdb=" C3' ATP A 901 " pdb=" O2' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C2' ATP F 901 " pdb=" C1' ATP F 901 " pdb=" C3' ATP F 901 " pdb=" O2' ATP F 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 5266 not shown) Planarity restraints: 6107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 554 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 555 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 555 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 555 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 234 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C LEU C 234 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU C 234 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG C 235 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 298 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LYS F 298 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS F 298 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA F 299 " -0.008 2.00e-02 2.50e+03 ... (remaining 6104 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.06: 8 2.06 - 2.77: 7002 2.77 - 3.48: 50746 3.48 - 4.19: 75257 4.19 - 4.90: 138570 Nonbonded interactions: 271583 Sorted by model distance: nonbonded pdb=" NZ LYS J 148 " pdb=" C GLY K 276 " model vdw 1.355 3.350 nonbonded pdb=" OG1 THR E 262 " pdb=" O3G ATP E 901 " model vdw 1.942 2.440 nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 1.953 2.440 nonbonded pdb=" O GLN K 262 " pdb=" OG SER K 265 " model vdw 1.953 2.440 nonbonded pdb=" OG1 THR F 458 " pdb=" OD1 ASP F 460 " model vdw 1.988 2.440 ... (remaining 271578 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 786 or resid 902)) selection = (chain 'C' and (resid 33 through 786 or resid 902)) } ncs_group { reference = (chain 'B' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'D' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'E' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'F' and (resid 208 through 787 or resid 901 through 902)) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 201 through 273) } 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 13.430 Check model and map are aligned: 0.520 Set scattering table: 0.280 Process input model: 95.160 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 0.110 34638 Z= 0.201 Angle : 0.547 10.715 46870 Z= 0.262 Chirality : 0.043 0.338 5269 Planarity : 0.003 0.038 6107 Dihedral : 11.257 142.777 13351 Min Nonbonded Distance : 1.355 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.89 % Allowed : 5.33 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 4259 helix: 2.23 (0.12), residues: 2036 sheet: -0.64 (0.21), residues: 615 loop : 0.30 (0.17), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 486 HIS 0.003 0.001 HIS G 208 PHE 0.010 0.001 PHE D 275 TYR 0.011 0.001 TYR B 254 ARG 0.003 0.000 ARG G 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 564 time to evaluate : 3.954 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: A 75 LYS cc_start: 0.7421 (mmtt) cc_final: 0.6857 (mmtt) REVERT: A 92 CYS cc_start: 0.6666 (p) cc_final: 0.6357 (p) REVERT: A 168 MET cc_start: 0.6996 (ppp) cc_final: 0.6731 (ppp) REVERT: A 305 LYS cc_start: 0.8289 (pptt) cc_final: 0.7930 (mmtt) REVERT: A 314 ASP cc_start: 0.8813 (t0) cc_final: 0.8604 (t0) REVERT: A 359 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8039 (mtp-110) REVERT: B 774 LEU cc_start: 0.8717 (tp) cc_final: 0.8452 (tp) REVERT: B 778 GLU cc_start: 0.8688 (tp30) cc_final: 0.8459 (pt0) REVERT: C 253 MET cc_start: 0.8341 (mtp) cc_final: 0.8023 (mtp) REVERT: C 430 MET cc_start: 0.8746 (tpt) cc_final: 0.8487 (tpp) REVERT: C 474 LEU cc_start: 0.8716 (mm) cc_final: 0.8416 (pt) REVERT: D 514 THR cc_start: 0.8739 (m) cc_final: 0.8501 (p) REVERT: D 556 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8081 (mp0) REVERT: E 314 ASP cc_start: 0.8893 (t0) cc_final: 0.8622 (t0) REVERT: E 359 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7163 (mtp85) REVERT: E 430 MET cc_start: 0.9198 (tpp) cc_final: 0.8985 (tpp) REVERT: E 556 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8410 (mt-10) REVERT: E 618 MET cc_start: 0.8977 (ttp) cc_final: 0.8665 (ttm) REVERT: F 246 LYS cc_start: 0.8017 (tptp) cc_final: 0.7742 (tmtt) REVERT: F 314 ASP cc_start: 0.8865 (t0) cc_final: 0.8520 (t0) REVERT: F 324 ASP cc_start: 0.6719 (t0) cc_final: 0.6518 (t0) REVERT: F 348 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7607 (mtm-85) REVERT: F 556 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8527 (mm-30) REVERT: G 254 TYR cc_start: 0.7742 (t80) cc_final: 0.7376 (t80) REVERT: G 293 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.8026 (tp-100) REVERT: G 316 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5654 (mm-30) REVERT: G 344 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7122 (p-80) REVERT: G 378 SER cc_start: 0.6989 (m) cc_final: 0.6763 (m) REVERT: G 445 TYR cc_start: 0.7802 (m-80) cc_final: 0.7159 (m-80) REVERT: G 553 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7527 (tttm) outliers start: 69 outliers final: 22 residues processed: 611 average time/residue: 0.5390 time to fit residues: 503.5254 Evaluate side-chains 325 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 300 time to evaluate : 5.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 129 optimal weight: 30.0000 chunk 203 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 387 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS C 206 ASN C 394 HIS D 207 ASN D 225 GLN ** E 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 ASN G 344 HIS G 361 HIS G 362 GLN G 528 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 34638 Z= 0.380 Angle : 0.660 9.166 46870 Z= 0.321 Chirality : 0.045 0.206 5269 Planarity : 0.004 0.040 6107 Dihedral : 9.828 136.419 4969 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.45 % Favored : 94.53 % Rotamer: Outliers : 2.49 % Allowed : 9.68 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 4259 helix: 1.80 (0.12), residues: 2044 sheet: -0.56 (0.21), residues: 594 loop : 0.27 (0.17), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 486 HIS 0.007 0.001 HIS A 716 PHE 0.023 0.002 PHE A 141 TYR 0.018 0.002 TYR C 254 ARG 0.008 0.001 ARG E 672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 303 time to evaluate : 3.783 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: A 168 MET cc_start: 0.6977 (ppp) cc_final: 0.5321 (mmt) REVERT: A 314 ASP cc_start: 0.8953 (t0) cc_final: 0.8686 (t0) REVERT: A 359 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8030 (mtm-85) REVERT: B 215 ASP cc_start: 0.9217 (t0) cc_final: 0.9010 (t0) REVERT: B 285 MET cc_start: 0.8982 (mmm) cc_final: 0.8772 (mmt) REVERT: B 348 ARG cc_start: 0.8302 (ptp90) cc_final: 0.8075 (ptp90) REVERT: B 574 ASP cc_start: 0.8714 (m-30) cc_final: 0.8514 (t0) REVERT: B 774 LEU cc_start: 0.8745 (tp) cc_final: 0.8480 (tp) REVERT: C 202 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6225 (tt0) REVERT: C 253 MET cc_start: 0.8423 (mtp) cc_final: 0.8085 (mtp) REVERT: C 474 LEU cc_start: 0.8776 (mm) cc_final: 0.8412 (pt) REVERT: D 348 ARG cc_start: 0.7063 (ptt-90) cc_final: 0.6758 (mtm180) REVERT: D 359 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.7798 (mtm-85) REVERT: D 514 THR cc_start: 0.8677 (m) cc_final: 0.8432 (p) REVERT: D 556 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8083 (mp0) REVERT: E 285 MET cc_start: 0.8827 (mmp) cc_final: 0.8601 (mmm) REVERT: E 378 ASP cc_start: 0.8241 (t0) cc_final: 0.8019 (t0) REVERT: E 556 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8305 (mt-10) REVERT: E 635 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7662 (mmm160) REVERT: E 689 THR cc_start: 0.8712 (p) cc_final: 0.8462 (p) REVERT: F 229 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7921 (ttm) REVERT: F 246 LYS cc_start: 0.8250 (tptp) cc_final: 0.7935 (tmtt) REVERT: F 315 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7714 (tp30) REVERT: F 324 ASP cc_start: 0.7032 (t0) cc_final: 0.6823 (t0) REVERT: G 553 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7619 (tttt) REVERT: H 238 MET cc_start: 0.8239 (ttm) cc_final: 0.7709 (tpp) outliers start: 91 outliers final: 50 residues processed: 376 average time/residue: 0.4845 time to fit residues: 295.9390 Evaluate side-chains 318 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 265 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 215 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 322 optimal weight: 2.9990 chunk 264 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 388 optimal weight: 0.8980 chunk 419 optimal weight: 2.9990 chunk 345 optimal weight: 7.9990 chunk 385 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 311 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS C 193 HIS D 548 ASN G 362 GLN G 491 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34638 Z= 0.175 Angle : 0.563 10.467 46870 Z= 0.270 Chirality : 0.042 0.147 5269 Planarity : 0.004 0.044 6107 Dihedral : 9.027 136.990 4943 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 2.38 % Allowed : 10.75 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 4259 helix: 1.80 (0.12), residues: 2052 sheet: -0.38 (0.21), residues: 608 loop : 0.34 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 486 HIS 0.003 0.001 HIS A 716 PHE 0.013 0.001 PHE G 340 TYR 0.016 0.001 TYR G 439 ARG 0.007 0.000 ARG F 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 299 time to evaluate : 4.072 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: A 168 MET cc_start: 0.6920 (ppp) cc_final: 0.5294 (mmt) REVERT: A 314 ASP cc_start: 0.8814 (t0) cc_final: 0.8552 (t0) REVERT: A 359 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8077 (mtp-110) REVERT: B 574 ASP cc_start: 0.8686 (m-30) cc_final: 0.8466 (t0) REVERT: C 202 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6153 (tt0) REVERT: C 253 MET cc_start: 0.8362 (mtp) cc_final: 0.8004 (mtp) REVERT: C 474 LEU cc_start: 0.8775 (mm) cc_final: 0.8417 (pt) REVERT: D 348 ARG cc_start: 0.6972 (ptt-90) cc_final: 0.6660 (mtm180) REVERT: D 514 THR cc_start: 0.8669 (m) cc_final: 0.8431 (p) REVERT: D 556 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8045 (mp0) REVERT: D 568 ASN cc_start: 0.7435 (t0) cc_final: 0.7101 (m110) REVERT: E 317 ASP cc_start: 0.8376 (t0) cc_final: 0.7874 (p0) REVERT: E 342 MET cc_start: 0.8681 (mtp) cc_final: 0.8383 (mtp) REVERT: E 378 ASP cc_start: 0.8228 (t0) cc_final: 0.8002 (t0) REVERT: E 587 ASP cc_start: 0.8090 (m-30) cc_final: 0.7878 (m-30) REVERT: E 635 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7767 (mmm160) REVERT: E 689 THR cc_start: 0.8764 (p) cc_final: 0.8510 (p) REVERT: E 752 TYR cc_start: 0.6658 (p90) cc_final: 0.6426 (p90) REVERT: F 246 LYS cc_start: 0.8148 (tptp) cc_final: 0.7939 (tmtt) REVERT: F 315 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7711 (tp30) REVERT: F 324 ASP cc_start: 0.6999 (t0) cc_final: 0.6771 (t0) REVERT: F 345 MET cc_start: 0.7914 (ttp) cc_final: 0.7464 (tmm) REVERT: F 782 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8710 (tm-30) REVERT: G 242 SER cc_start: 0.8582 (m) cc_final: 0.8038 (t) REVERT: G 254 TYR cc_start: 0.7854 (t80) cc_final: 0.7497 (t80) REVERT: H 238 MET cc_start: 0.8275 (ttm) cc_final: 0.7714 (tpp) outliers start: 87 outliers final: 54 residues processed: 370 average time/residue: 0.4605 time to fit residues: 281.1819 Evaluate side-chains 324 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 268 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 383 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 389 optimal weight: 2.9990 chunk 412 optimal weight: 0.3980 chunk 203 optimal weight: 0.0970 chunk 369 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS A 719 HIS C 337 GLN F 295 ASN G 362 GLN G 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34638 Z= 0.248 Angle : 0.577 10.913 46870 Z= 0.276 Chirality : 0.042 0.233 5269 Planarity : 0.004 0.044 6107 Dihedral : 8.830 138.481 4941 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 2.73 % Allowed : 11.40 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.14), residues: 4259 helix: 1.73 (0.12), residues: 2041 sheet: -0.29 (0.21), residues: 605 loop : 0.28 (0.17), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 486 HIS 0.007 0.001 HIS A 716 PHE 0.017 0.001 PHE G 340 TYR 0.018 0.001 TYR G 439 ARG 0.007 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 280 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: A 168 MET cc_start: 0.7043 (ppp) cc_final: 0.5335 (mmt) REVERT: A 314 ASP cc_start: 0.8912 (t0) cc_final: 0.8689 (t0) REVERT: A 331 GLU cc_start: 0.6926 (pt0) cc_final: 0.6515 (pt0) REVERT: A 359 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.8052 (mtm-85) REVERT: A 398 MET cc_start: 0.9190 (mtp) cc_final: 0.8634 (mtp) REVERT: B 293 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: B 342 MET cc_start: 0.9143 (mtp) cc_final: 0.8438 (mtp) REVERT: B 574 ASP cc_start: 0.8729 (m-30) cc_final: 0.8454 (t0) REVERT: C 202 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6062 (tt0) REVERT: C 253 MET cc_start: 0.8372 (mtp) cc_final: 0.8018 (mtp) REVERT: C 474 LEU cc_start: 0.8799 (mm) cc_final: 0.8386 (pt) REVERT: D 348 ARG cc_start: 0.6857 (ptt-90) cc_final: 0.6537 (mtm180) REVERT: D 359 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.7799 (mtm-85) REVERT: D 514 THR cc_start: 0.8683 (m) cc_final: 0.8444 (p) REVERT: D 556 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8065 (mp0) REVERT: D 568 ASN cc_start: 0.7533 (t0) cc_final: 0.7026 (m110) REVERT: E 229 MET cc_start: 0.9074 (tpt) cc_final: 0.8547 (tpt) REVERT: E 254 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8005 (p90) REVERT: E 317 ASP cc_start: 0.8434 (t0) cc_final: 0.8003 (p0) REVERT: E 332 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7660 (ttm-80) REVERT: E 342 MET cc_start: 0.8773 (mtp) cc_final: 0.8285 (mtp) REVERT: E 476 GLU cc_start: 0.8110 (mp0) cc_final: 0.7846 (pt0) REVERT: E 635 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7722 (mmm160) REVERT: E 689 THR cc_start: 0.8804 (p) cc_final: 0.8563 (p) REVERT: E 752 TYR cc_start: 0.6743 (p90) cc_final: 0.6520 (p90) REVERT: F 223 MET cc_start: 0.8813 (tpp) cc_final: 0.8429 (tpp) REVERT: F 315 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7716 (tp30) REVERT: F 324 ASP cc_start: 0.7123 (t0) cc_final: 0.6562 (t0) REVERT: F 325 LYS cc_start: 0.8014 (mmpt) cc_final: 0.7593 (mmmt) REVERT: F 785 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7923 (tppt) REVERT: G 242 SER cc_start: 0.8598 (m) cc_final: 0.8104 (t) REVERT: H 238 MET cc_start: 0.8287 (ttm) cc_final: 0.7694 (tpp) outliers start: 100 outliers final: 63 residues processed: 365 average time/residue: 0.4482 time to fit residues: 270.6532 Evaluate side-chains 335 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 266 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 343 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 285 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 210 optimal weight: 0.7980 chunk 370 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34638 Z= 0.195 Angle : 0.553 11.675 46870 Z= 0.264 Chirality : 0.042 0.224 5269 Planarity : 0.004 0.044 6107 Dihedral : 8.539 138.875 4936 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 2.82 % Allowed : 12.03 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 4259 helix: 1.75 (0.12), residues: 2039 sheet: -0.23 (0.21), residues: 608 loop : 0.29 (0.17), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 486 HIS 0.007 0.001 HIS A 716 PHE 0.024 0.001 PHE E 585 TYR 0.018 0.001 TYR G 439 ARG 0.005 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 283 time to evaluate : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7109 (ppp) cc_final: 0.5410 (mmt) REVERT: A 200 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.7164 (p0) REVERT: A 314 ASP cc_start: 0.8884 (t0) cc_final: 0.8669 (t0) REVERT: A 359 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8057 (mtp-110) REVERT: A 398 MET cc_start: 0.9190 (mtp) cc_final: 0.8669 (mtp) REVERT: A 618 MET cc_start: 0.8838 (ttp) cc_final: 0.8599 (ttp) REVERT: B 208 MET cc_start: 0.5308 (mmp) cc_final: 0.4830 (tpt) REVERT: B 293 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: B 332 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7811 (mtt90) REVERT: B 342 MET cc_start: 0.9104 (mtp) cc_final: 0.8344 (mtp) REVERT: B 556 GLU cc_start: 0.8633 (tp30) cc_final: 0.8353 (tp30) REVERT: B 574 ASP cc_start: 0.8705 (m-30) cc_final: 0.8429 (t0) REVERT: C 474 LEU cc_start: 0.8723 (mm) cc_final: 0.8393 (pt) REVERT: D 359 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.7917 (mtm-85) REVERT: D 514 THR cc_start: 0.8666 (m) cc_final: 0.8432 (p) REVERT: D 556 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8076 (mp0) REVERT: D 568 ASN cc_start: 0.7533 (t0) cc_final: 0.6999 (m110) REVERT: E 229 MET cc_start: 0.9137 (tpt) cc_final: 0.8670 (tpt) REVERT: E 254 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8025 (p90) REVERT: E 285 MET cc_start: 0.8671 (mmm) cc_final: 0.8421 (mmm) REVERT: E 317 ASP cc_start: 0.8446 (t0) cc_final: 0.8028 (p0) REVERT: E 332 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7665 (ttm-80) REVERT: E 342 MET cc_start: 0.8749 (mtp) cc_final: 0.8202 (mtp) REVERT: E 476 GLU cc_start: 0.8061 (mp0) cc_final: 0.7811 (pt0) REVERT: E 635 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7735 (mmm160) REVERT: E 689 THR cc_start: 0.8813 (p) cc_final: 0.8567 (p) REVERT: E 752 TYR cc_start: 0.6747 (p90) cc_final: 0.6520 (p90) REVERT: F 223 MET cc_start: 0.8788 (tpp) cc_final: 0.8428 (tpp) REVERT: F 315 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7669 (tp30) REVERT: F 324 ASP cc_start: 0.7177 (t0) cc_final: 0.6605 (t0) REVERT: F 325 LYS cc_start: 0.7979 (mmpt) cc_final: 0.7553 (mmmt) REVERT: F 785 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7963 (tppt) REVERT: G 242 SER cc_start: 0.8561 (m) cc_final: 0.7988 (t) outliers start: 103 outliers final: 61 residues processed: 366 average time/residue: 0.4878 time to fit residues: 296.9597 Evaluate side-chains 330 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 262 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 203 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 138 optimal weight: 5.9990 chunk 371 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 242 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 413 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34638 Z= 0.177 Angle : 0.552 13.247 46870 Z= 0.261 Chirality : 0.041 0.180 5269 Planarity : 0.004 0.045 6107 Dihedral : 8.388 138.849 4934 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 2.65 % Allowed : 12.47 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 4259 helix: 1.77 (0.12), residues: 2042 sheet: -0.14 (0.21), residues: 608 loop : 0.29 (0.17), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 486 HIS 0.007 0.001 HIS A 716 PHE 0.020 0.001 PHE E 585 TYR 0.018 0.001 TYR G 439 ARG 0.006 0.000 ARG A 717 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 271 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7106 (ppp) cc_final: 0.5403 (mmt) REVERT: A 359 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8070 (mtp-110) REVERT: A 398 MET cc_start: 0.9161 (mtp) cc_final: 0.8660 (mtp) REVERT: A 618 MET cc_start: 0.8811 (ttp) cc_final: 0.8531 (ttp) REVERT: B 208 MET cc_start: 0.5389 (mmp) cc_final: 0.4929 (tpt) REVERT: B 293 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: B 342 MET cc_start: 0.9095 (mtp) cc_final: 0.8329 (mtp) REVERT: B 348 ARG cc_start: 0.8197 (ptp90) cc_final: 0.7929 (ptp90) REVERT: B 574 ASP cc_start: 0.8712 (m-30) cc_final: 0.8434 (t0) REVERT: C 474 LEU cc_start: 0.8717 (mm) cc_final: 0.8393 (pt) REVERT: D 514 THR cc_start: 0.8656 (m) cc_final: 0.8421 (p) REVERT: D 556 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8028 (mp0) REVERT: D 568 ASN cc_start: 0.7585 (t0) cc_final: 0.7032 (m-40) REVERT: D 784 MET cc_start: 0.8367 (mmm) cc_final: 0.8116 (mmm) REVERT: E 223 MET cc_start: 0.8546 (tpp) cc_final: 0.8231 (mmm) REVERT: E 229 MET cc_start: 0.9125 (tpt) cc_final: 0.8638 (tpt) REVERT: E 254 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8036 (p90) REVERT: E 285 MET cc_start: 0.8685 (mmm) cc_final: 0.8446 (mmm) REVERT: E 317 ASP cc_start: 0.8429 (t0) cc_final: 0.8023 (p0) REVERT: E 332 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7661 (ttm-80) REVERT: E 342 MET cc_start: 0.8750 (mtp) cc_final: 0.8337 (mtp) REVERT: E 617 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: E 635 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7760 (mmm160) REVERT: E 689 THR cc_start: 0.8817 (p) cc_final: 0.8574 (p) REVERT: E 752 TYR cc_start: 0.6760 (p90) cc_final: 0.6525 (p90) REVERT: F 315 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7669 (tp30) REVERT: F 324 ASP cc_start: 0.7149 (t0) cc_final: 0.6549 (t0) REVERT: F 325 LYS cc_start: 0.7982 (mmpt) cc_final: 0.7549 (mmmt) REVERT: F 785 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7975 (tppt) REVERT: G 242 SER cc_start: 0.8507 (m) cc_final: 0.8064 (t) REVERT: G 344 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7147 (p90) REVERT: G 440 MET cc_start: 0.8394 (ttt) cc_final: 0.8191 (mtt) outliers start: 97 outliers final: 68 residues processed: 352 average time/residue: 0.4516 time to fit residues: 262.4897 Evaluate side-chains 340 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 265 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 533 ILE Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 203 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 398 optimal weight: 0.0020 chunk 46 optimal weight: 2.9990 chunk 235 optimal weight: 0.1980 chunk 301 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 347 optimal weight: 6.9990 chunk 230 optimal weight: 0.1980 chunk 411 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 206 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34638 Z= 0.174 Angle : 0.550 15.106 46870 Z= 0.259 Chirality : 0.041 0.162 5269 Planarity : 0.004 0.045 6107 Dihedral : 8.268 138.628 4934 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 2.49 % Allowed : 12.93 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.14), residues: 4259 helix: 1.78 (0.12), residues: 2041 sheet: -0.07 (0.21), residues: 606 loop : 0.29 (0.17), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 486 HIS 0.009 0.001 HIS A 716 PHE 0.016 0.001 PHE E 585 TYR 0.017 0.001 TYR G 439 ARG 0.009 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 276 time to evaluate : 3.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7093 (ppp) cc_final: 0.5394 (mmt) REVERT: A 200 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7154 (p0) REVERT: A 331 GLU cc_start: 0.6924 (pt0) cc_final: 0.6569 (tt0) REVERT: A 359 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.8061 (mtp-110) REVERT: A 398 MET cc_start: 0.9180 (mtp) cc_final: 0.8692 (mtp) REVERT: B 208 MET cc_start: 0.5310 (mmp) cc_final: 0.4810 (tpt) REVERT: B 293 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: B 342 MET cc_start: 0.9086 (mtp) cc_final: 0.8306 (mtp) REVERT: B 574 ASP cc_start: 0.8711 (m-30) cc_final: 0.8436 (t0) REVERT: C 474 LEU cc_start: 0.8705 (mm) cc_final: 0.8344 (pt) REVERT: D 285 MET cc_start: 0.8533 (mmm) cc_final: 0.8203 (mmm) REVERT: D 359 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.7740 (mtm-85) REVERT: D 514 THR cc_start: 0.8667 (m) cc_final: 0.8442 (p) REVERT: D 556 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8037 (mp0) REVERT: D 568 ASN cc_start: 0.7625 (t0) cc_final: 0.7072 (m110) REVERT: D 784 MET cc_start: 0.8366 (mmm) cc_final: 0.8156 (mmm) REVERT: E 223 MET cc_start: 0.8485 (tpp) cc_final: 0.8195 (mmm) REVERT: E 229 MET cc_start: 0.9132 (tpt) cc_final: 0.8642 (tpt) REVERT: E 254 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8106 (p90) REVERT: E 285 MET cc_start: 0.8705 (mmm) cc_final: 0.8471 (mmm) REVERT: E 317 ASP cc_start: 0.8407 (t0) cc_final: 0.8028 (p0) REVERT: E 332 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7660 (ttm-80) REVERT: E 342 MET cc_start: 0.8762 (mtp) cc_final: 0.8343 (mtp) REVERT: E 476 GLU cc_start: 0.8044 (mp0) cc_final: 0.7777 (pt0) REVERT: E 617 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: E 635 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7788 (mmm160) REVERT: E 689 THR cc_start: 0.8827 (p) cc_final: 0.8583 (p) REVERT: E 752 TYR cc_start: 0.6751 (p90) cc_final: 0.6507 (p90) REVERT: F 315 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8055 (mm-30) REVERT: F 324 ASP cc_start: 0.7177 (t0) cc_final: 0.6550 (t0) REVERT: F 325 LYS cc_start: 0.7986 (mmpt) cc_final: 0.7548 (mmmt) REVERT: F 785 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8015 (tppt) REVERT: G 242 SER cc_start: 0.8577 (m) cc_final: 0.8031 (t) REVERT: G 344 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.6905 (p90) REVERT: G 440 MET cc_start: 0.8444 (ttt) cc_final: 0.8237 (mtt) outliers start: 91 outliers final: 71 residues processed: 349 average time/residue: 0.4560 time to fit residues: 263.3757 Evaluate side-chains 342 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 263 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 533 ILE Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 254 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 203 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 323 optimal weight: 0.2980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN G 426 ASN H 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 34638 Z= 0.339 Angle : 0.621 15.325 46870 Z= 0.300 Chirality : 0.043 0.244 5269 Planarity : 0.004 0.045 6107 Dihedral : 8.400 141.069 4934 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.26 % Favored : 94.72 % Rotamer: Outliers : 2.87 % Allowed : 13.13 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 4259 helix: 1.61 (0.12), residues: 2038 sheet: -0.25 (0.21), residues: 598 loop : 0.18 (0.17), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 486 HIS 0.012 0.001 HIS A 716 PHE 0.018 0.002 PHE G 169 TYR 0.019 0.001 TYR G 439 ARG 0.007 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 261 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7220 (ppp) cc_final: 0.5414 (mmt) REVERT: A 200 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7180 (p0) REVERT: A 331 GLU cc_start: 0.7102 (pt0) cc_final: 0.6767 (tt0) REVERT: A 359 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8041 (mtp-110) REVERT: B 293 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: B 348 ARG cc_start: 0.8258 (ptp90) cc_final: 0.8057 (ptp90) REVERT: B 574 ASP cc_start: 0.8759 (m-30) cc_final: 0.8486 (t0) REVERT: C 474 LEU cc_start: 0.8822 (mm) cc_final: 0.8346 (pt) REVERT: D 285 MET cc_start: 0.8615 (mmm) cc_final: 0.8301 (mmm) REVERT: D 359 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.7776 (mtm-85) REVERT: D 514 THR cc_start: 0.8656 (m) cc_final: 0.8426 (p) REVERT: D 556 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8040 (mp0) REVERT: D 568 ASN cc_start: 0.7689 (t0) cc_final: 0.7184 (m110) REVERT: D 784 MET cc_start: 0.8405 (mmm) cc_final: 0.8152 (mmm) REVERT: E 223 MET cc_start: 0.8526 (tpp) cc_final: 0.8276 (mmm) REVERT: E 229 MET cc_start: 0.9140 (tpt) cc_final: 0.8724 (tpt) REVERT: E 254 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7990 (p90) REVERT: E 317 ASP cc_start: 0.8491 (t0) cc_final: 0.8072 (p0) REVERT: E 332 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7672 (ttm-80) REVERT: E 342 MET cc_start: 0.8829 (mtp) cc_final: 0.8493 (mtp) REVERT: E 617 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: E 635 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7761 (mmm160) REVERT: E 689 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8656 (p) REVERT: F 315 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7652 (tp30) REVERT: F 324 ASP cc_start: 0.7387 (t0) cc_final: 0.6818 (t0) REVERT: F 325 LYS cc_start: 0.7999 (mmpt) cc_final: 0.7576 (mmmt) REVERT: F 785 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7996 (tppt) REVERT: G 242 SER cc_start: 0.8701 (m) cc_final: 0.8116 (t) REVERT: G 378 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7546 (p) REVERT: G 440 MET cc_start: 0.8521 (ttt) cc_final: 0.8303 (mtt) REVERT: H 281 MET cc_start: 0.2354 (mmp) cc_final: 0.2038 (mmp) outliers start: 105 outliers final: 71 residues processed: 348 average time/residue: 0.4681 time to fit residues: 271.4929 Evaluate side-chains 335 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 255 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 533 ILE Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain K residue 203 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 374 optimal weight: 0.8980 chunk 394 optimal weight: 0.9990 chunk 359 optimal weight: 3.9990 chunk 383 optimal weight: 0.9990 chunk 230 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 346 optimal weight: 0.9980 chunk 362 optimal weight: 2.9990 chunk 382 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34638 Z= 0.179 Angle : 0.563 16.480 46870 Z= 0.266 Chirality : 0.041 0.161 5269 Planarity : 0.004 0.045 6107 Dihedral : 8.213 141.357 4934 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.41 % Allowed : 13.86 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 4259 helix: 1.67 (0.12), residues: 2043 sheet: -0.14 (0.21), residues: 602 loop : 0.25 (0.17), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 486 HIS 0.003 0.001 HIS G 521 PHE 0.012 0.001 PHE E 585 TYR 0.018 0.001 TYR G 439 ARG 0.006 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 265 time to evaluate : 4.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7201 (ppp) cc_final: 0.5409 (mmt) REVERT: A 200 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7172 (p0) REVERT: A 283 GLU cc_start: 0.8138 (tt0) cc_final: 0.7770 (tt0) REVERT: A 331 GLU cc_start: 0.7074 (pt0) cc_final: 0.6775 (tt0) REVERT: A 359 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8084 (mtp-110) REVERT: B 208 MET cc_start: 0.5363 (mmp) cc_final: 0.4959 (tpt) REVERT: B 293 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: B 342 MET cc_start: 0.9074 (mtp) cc_final: 0.8277 (mtp) REVERT: B 348 ARG cc_start: 0.8328 (ptp90) cc_final: 0.8098 (ptp90) REVERT: B 574 ASP cc_start: 0.8717 (m-30) cc_final: 0.8430 (t0) REVERT: C 464 PHE cc_start: 0.8562 (t80) cc_final: 0.8165 (t80) REVERT: C 474 LEU cc_start: 0.8705 (mm) cc_final: 0.8368 (pt) REVERT: D 285 MET cc_start: 0.8581 (mmm) cc_final: 0.8274 (mmm) REVERT: D 359 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.7792 (mtm-85) REVERT: D 514 THR cc_start: 0.8662 (m) cc_final: 0.8428 (p) REVERT: D 556 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8010 (mp0) REVERT: D 568 ASN cc_start: 0.7639 (t0) cc_final: 0.7125 (m110) REVERT: E 229 MET cc_start: 0.9148 (tpt) cc_final: 0.8754 (tpt) REVERT: E 254 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8034 (p90) REVERT: E 317 ASP cc_start: 0.8476 (t0) cc_final: 0.8057 (p0) REVERT: E 332 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7661 (ttm-80) REVERT: E 617 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: E 635 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7830 (mmm160) REVERT: E 689 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8586 (p) REVERT: F 315 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7642 (tp30) REVERT: F 324 ASP cc_start: 0.7352 (t0) cc_final: 0.6889 (t0) REVERT: F 325 LYS cc_start: 0.7961 (mmpt) cc_final: 0.7559 (mmmt) REVERT: F 785 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8041 (tppt) REVERT: G 242 SER cc_start: 0.8602 (m) cc_final: 0.8048 (t) REVERT: G 344 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.6864 (p90) REVERT: G 422 MET cc_start: 0.8222 (tpp) cc_final: 0.7667 (mmm) REVERT: G 440 MET cc_start: 0.8484 (ttt) cc_final: 0.8281 (mtt) REVERT: G 570 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8027 (mm-40) REVERT: H 281 MET cc_start: 0.2336 (mmp) cc_final: 0.2018 (mmp) outliers start: 88 outliers final: 67 residues processed: 338 average time/residue: 0.4788 time to fit residues: 266.7230 Evaluate side-chains 332 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 255 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 533 ILE Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 0.9980 chunk 405 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 425 optimal weight: 0.0370 chunk 391 optimal weight: 1.9990 chunk 338 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 ASN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34638 Z= 0.169 Angle : 0.556 16.716 46870 Z= 0.262 Chirality : 0.041 0.188 5269 Planarity : 0.004 0.044 6107 Dihedral : 8.063 140.951 4934 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.77 % Favored : 95.21 % Rotamer: Outliers : 2.27 % Allowed : 14.03 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.14), residues: 4259 helix: 1.74 (0.12), residues: 2041 sheet: -0.03 (0.21), residues: 600 loop : 0.30 (0.17), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 486 HIS 0.003 0.000 HIS G 521 PHE 0.016 0.001 PHE G 340 TYR 0.017 0.001 TYR G 439 ARG 0.006 0.000 ARG D 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 266 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7190 (ppp) cc_final: 0.5398 (mmt) REVERT: A 200 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7180 (p0) REVERT: A 283 GLU cc_start: 0.8095 (tt0) cc_final: 0.7741 (tt0) REVERT: A 359 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8090 (mtp-110) REVERT: B 208 MET cc_start: 0.5416 (mmp) cc_final: 0.4952 (tpt) REVERT: B 293 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: B 342 MET cc_start: 0.9057 (mtp) cc_final: 0.8296 (mtp) REVERT: B 348 ARG cc_start: 0.8339 (ptp90) cc_final: 0.8123 (ptp90) REVERT: B 574 ASP cc_start: 0.8713 (m-30) cc_final: 0.8406 (t0) REVERT: C 464 PHE cc_start: 0.8522 (t80) cc_final: 0.8093 (t80) REVERT: C 474 LEU cc_start: 0.8700 (mm) cc_final: 0.8345 (pt) REVERT: D 285 MET cc_start: 0.8576 (mmm) cc_final: 0.8264 (mmm) REVERT: D 359 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.7778 (mtm-85) REVERT: D 514 THR cc_start: 0.8630 (m) cc_final: 0.8423 (p) REVERT: D 556 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8045 (mp0) REVERT: D 568 ASN cc_start: 0.7649 (t0) cc_final: 0.7137 (m-40) REVERT: E 229 MET cc_start: 0.9155 (tpt) cc_final: 0.8708 (tpt) REVERT: E 254 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8137 (p90) REVERT: E 264 MET cc_start: 0.8151 (ttm) cc_final: 0.7834 (ttm) REVERT: E 317 ASP cc_start: 0.8474 (t0) cc_final: 0.8070 (p0) REVERT: E 332 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7661 (ttm-80) REVERT: E 476 GLU cc_start: 0.8060 (mp0) cc_final: 0.7798 (pt0) REVERT: E 617 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: E 635 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7826 (mmm160) REVERT: E 689 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8648 (p) REVERT: F 315 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7666 (tp30) REVERT: F 324 ASP cc_start: 0.7343 (t0) cc_final: 0.6853 (t0) REVERT: F 325 LYS cc_start: 0.7929 (mmpt) cc_final: 0.7518 (mmmt) REVERT: F 785 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8033 (tppt) REVERT: G 242 SER cc_start: 0.8588 (m) cc_final: 0.8023 (t) REVERT: G 344 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.6792 (p90) REVERT: G 422 MET cc_start: 0.8190 (tpp) cc_final: 0.7646 (mmm) REVERT: G 440 MET cc_start: 0.8461 (ttt) cc_final: 0.8259 (mtt) REVERT: G 570 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8055 (mm-40) REVERT: H 281 MET cc_start: 0.2229 (mmp) cc_final: 0.1910 (mmp) outliers start: 83 outliers final: 66 residues processed: 336 average time/residue: 0.4658 time to fit residues: 259.5586 Evaluate side-chains 335 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 259 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 533 ILE Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 269 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 312 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 339 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 348 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 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 = 0.3951 r_free = 0.3951 target = 0.119405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089142 restraints weight = 86939.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091894 restraints weight = 44559.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092502 restraints weight = 28277.592| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34638 Z= 0.185 Angle : 0.565 17.804 46870 Z= 0.265 Chirality : 0.041 0.177 5269 Planarity : 0.004 0.044 6107 Dihedral : 8.006 139.468 4934 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 2.19 % Allowed : 14.14 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.14), residues: 4259 helix: 1.76 (0.12), residues: 2035 sheet: 0.01 (0.21), residues: 600 loop : 0.30 (0.17), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 486 HIS 0.003 0.001 HIS G 521 PHE 0.012 0.001 PHE E 585 TYR 0.017 0.001 TYR G 439 ARG 0.006 0.000 ARG D 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6967.95 seconds wall clock time: 127 minutes 26.03 seconds (7646.03 seconds total)