Starting phenix.real_space_refine on Sun Jun 29 11:42:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8das_27274/06_2025/8das_27274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8das_27274/06_2025/8das_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/cci-nas-00/data/ceres_data/8das_27274/06_2025/8das_27274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8das_27274/06_2025/8das_27274.map" model { file = "/net/cci-nas-00/data/ceres_data/8das_27274/06_2025/8das_27274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8das_27274/06_2025/8das_27274.cif" } 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. Time to flip 2 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 19.67, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.49 Conformation dependent library (CDL) restraints added in 4.8 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... Secondary structure from input PDB file: 209 helices and 24 sheets defined 53.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 130 through 134 removed outlier: 4.041A pdb=" N GLU A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 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 201 through 205 removed outlier: 3.596A pdb=" N GLU A 204 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 220 through 236 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 237 through 244 removed outlier: 3.597A pdb=" N LYS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 329 through 346 removed outlier: 4.147A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 4.054A pdb=" N ILE A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 417 through 437 Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.546A pdb=" N PHE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 492 through 509 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 509 through 517 removed outlier: 3.762A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 546 removed outlier: 3.746A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.551A pdb=" N ILE A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 659 through 671 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 693 through 719 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.708A pdb=" N PHE A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 786 Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 219 through 236 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 244 removed outlier: 3.583A pdb=" N LYS B 241 " --> pdb=" O PRO B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.506A pdb=" N VAL B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 removed outlier: 4.240A pdb=" N SER B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) 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 315 through 319 Processing helix chain 'B' and resid 328 through 346 removed outlier: 3.588A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 346 " --> pdb=" O MET B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 395 Processing helix chain 'B' and resid 405 through 413 Processing helix chain 'B' and resid 417 through 437 Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 492 through 509 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 509 through 517 removed outlier: 3.946A pdb=" N TYR B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'B' and resid 553 through 562 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 588 through 593 removed outlier: 4.372A pdb=" N ILE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 659 through 672 Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 693 through 719 Processing helix chain 'B' and resid 754 through 765 removed outlier: 3.809A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 788 Processing helix chain 'C' and resid 52 through 59 Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 139 through 150 removed outlier: 4.130A pdb=" N LYS C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Proline residue: C 147 - end of helix removed outlier: 3.701A pdb=" N VAL C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.896A pdb=" N GLU C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 219 through 236 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 244 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.667A pdb=" N VAL C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 328 through 345 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 364 through 368 Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 405 through 413 removed outlier: 3.519A pdb=" N LEU C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 436 Processing helix chain 'C' and resid 437 through 440 Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 472 through 476 Processing helix chain 'C' and resid 492 through 509 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 509 through 517 removed outlier: 3.745A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.506A pdb=" N VAL C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 563 Processing helix chain 'C' and resid 568 through 579 Processing helix chain 'C' and resid 588 through 592 Processing helix chain 'C' and resid 609 through 621 Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 659 through 671 Processing helix chain 'C' and resid 682 through 689 Processing helix chain 'C' and resid 693 through 719 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.681A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 788 Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.651A pdb=" N ILE D 216 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 236 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 244 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 328 through 346 removed outlier: 4.346A pdb=" N LYS D 346 " --> pdb=" O MET D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 383 through 395 Processing helix chain 'D' and resid 405 through 413 Processing helix chain 'D' and resid 417 through 437 Processing helix chain 'D' and resid 438 through 440 No H-bonds generated for 'chain 'D' and resid 438 through 440' Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 472 through 476 Processing helix chain 'D' and resid 492 through 509 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 509 through 517 removed outlier: 3.876A pdb=" N TYR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.674A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 563 Processing helix chain 'D' and resid 568 through 579 Processing helix chain 'D' and resid 609 through 621 Processing helix chain 'D' and resid 659 through 671 Processing helix chain 'D' and resid 682 through 689 Processing helix chain 'D' and resid 693 through 719 Processing helix chain 'D' and resid 754 through 764 removed outlier: 3.952A pdb=" N PHE D 758 " --> pdb=" O THR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 787 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 219 through 236 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 236 through 244 removed outlier: 4.418A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 291 through 306 removed outlier: 3.729A pdb=" N ASN E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 319 Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.589A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) 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) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 417 through 437 Processing helix chain 'E' and resid 448 through 454 Processing helix chain 'E' and resid 458 through 469 removed outlier: 3.509A pdb=" N PHE E 462 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 476 Processing helix chain 'E' and resid 492 through 509 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 509 through 517 removed outlier: 3.796A pdb=" N TYR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 568 through 579 Processing helix chain 'E' and resid 609 through 621 Processing helix chain 'E' and resid 640 through 645 Processing helix chain 'E' and resid 659 through 671 Processing helix chain 'E' and resid 672 through 674 No H-bonds generated for 'chain 'E' and resid 672 through 674' Processing helix chain 'E' and resid 682 through 689 Processing helix chain 'E' and resid 693 through 719 Processing helix chain 'E' and resid 754 through 764 removed outlier: 3.515A pdb=" N PHE E 758 " --> pdb=" O THR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 787 removed outlier: 3.513A pdb=" N LEU E 774 " --> pdb=" O SER E 770 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 236 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 236 through 244 removed outlier: 4.441A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 290 through 306 removed outlier: 4.146A pdb=" N SER F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 326 Processing helix chain 'F' and resid 328 through 345 Processing helix chain 'F' and resid 346 through 348 No H-bonds generated for 'chain 'F' and resid 346 through 348' Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 383 through 395 Processing helix chain 'F' and resid 405 through 413 Processing helix chain 'F' and resid 417 through 437 Processing helix chain 'F' and resid 438 through 440 No H-bonds generated for 'chain 'F' and resid 438 through 440' Processing helix chain 'F' and resid 448 through 455 removed outlier: 3.527A pdb=" N LEU F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 468 Processing helix chain 'F' and resid 472 through 476 removed outlier: 3.523A pdb=" N GLU F 476 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 509 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 509 through 517 removed outlier: 4.106A pdb=" N TYR F 513 " --> pdb=" O HIS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 Processing helix chain 'F' and resid 553 through 563 Processing helix chain 'F' and resid 568 through 579 Processing helix chain 'F' and resid 588 through 592 Processing helix chain 'F' and resid 609 through 620 Processing helix chain 'F' and resid 640 through 645 Processing helix chain 'F' and resid 659 through 671 Processing helix chain 'F' and resid 682 through 688 Processing helix chain 'F' and resid 693 through 719 Processing helix chain 'F' and resid 754 through 763 Processing helix chain 'F' and resid 770 through 787 Processing helix chain 'G' and resid 116 through 125 removed outlier: 3.525A pdb=" N GLU G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.573A pdb=" N ALA G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 214 Processing helix chain 'G' and resid 242 through 256 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 299 through 318 removed outlier: 3.818A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'G' and resid 402 through 409 Processing helix chain 'G' and resid 460 through 463 removed outlier: 3.981A pdb=" N LEU G 463 " --> pdb=" O ASP G 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 460 through 463' Processing helix chain 'G' and resid 500 through 509 Processing helix chain 'G' and resid 509 through 515 removed outlier: 3.570A pdb=" N SER G 514 " --> pdb=" O ASN G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 523 Processing helix chain 'G' and resid 526 through 537 removed outlier: 3.631A pdb=" N GLN G 537 " --> pdb=" O ILE G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 552 Processing helix chain 'G' and resid 556 through 566 Processing helix chain 'G' and resid 566 through 579 removed outlier: 3.677A pdb=" N GLN G 570 " --> pdb=" O SER G 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 253 Processing helix chain 'J' and resid 122 through 135 removed outlier: 3.637A pdb=" N VAL J 126 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 160 removed outlier: 4.401A pdb=" N TYR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 235 removed outlier: 3.941A pdb=" N VAL K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 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: 4.093A pdb=" N VAL A 110 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 36 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 156 removed outlier: 4.734A pdb=" N ALA A 187 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ARG A 123 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 11.063A pdb=" N ASP A 189 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N SER A 125 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N ILE A 191 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N LEU A 127 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N HIS A 193 " --> pdb=" O LEU A 127 " (cutoff:3.500A) 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=AA3, first strand: chain 'A' and resid 275 through 279 removed outlier: 3.542A pdb=" N VAL A 352 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL A 251 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR A 357 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET A 253 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 252 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 removed outlier: 3.730A pdb=" N GLU A 480 " --> pdb=" O PHE A 549 " (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=AA5, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.411A pdb=" N GLY B 250 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL B 377 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (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) removed outlier: 6.679A pdb=" N PHE B 276 " --> pdb=" O ILE G 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 548 through 552 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) removed outlier: 6.619A pdb=" N VAL B 524 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR B 633 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE B 526 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AA8, 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) removed outlier: 5.775A pdb=" N VAL C 175 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU C 127 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 124 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing sheet with id=AA9, 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=AB1, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.387A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) 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) Processing sheet with id=AB2, first strand: chain 'C' and resid 548 through 552 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: 6.368A pdb=" N LEU C 525 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 275 through 280 removed outlier: 6.907A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (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) removed outlier: 3.958A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 548 through 552 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) 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) Processing sheet with id=AB5, first strand: chain 'E' and resid 312 through 314 removed outlier: 7.485A pdb=" N ILE E 313 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY E 250 " --> pdb=" O ARG E 375 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL E 377 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU E 252 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 479 through 480 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: 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) Processing sheet with id=AB7, first strand: chain 'F' and resid 275 through 280 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: 6.400A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 548 through 552 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) Processing sheet with id=AB9, first strand: chain 'G' and resid 224 through 226 removed outlier: 6.233A pdb=" N ILE G 224 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET G 440 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU G 226 " --> pdb=" O MET G 440 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N SER G 442 " --> pdb=" O LEU G 226 " (cutoff:3.500A) 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=AC1, first strand: chain 'G' and resid 382 through 386 removed outlier: 6.806A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER G 266 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL G 281 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER G 268 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA G 279 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N TYR G 270 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE G 277 " --> pdb=" O TYR G 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 295 through 297 Processing sheet with id=AC3, first strand: chain 'G' and resid 399 through 400 Processing sheet with id=AC4, 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=AC5, first strand: chain 'J' and resid 112 through 116 removed outlier: 3.893A pdb=" N SER J 165 " --> pdb=" O GLN J 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 212 through 216 removed outlier: 4.026A pdb=" N SER K 265 " --> pdb=" O GLN K 202 " (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) 1586 hydrogen bonds defined for protein. 4503 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: 16.38 Time building geometry restraints manager: 12.20 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: 0.00 - 2.14: 46370 2.14 - 4.29: 395 4.29 - 6.43: 74 6.43 - 8.57: 17 8.57 - 10.72: 14 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: 1.94 - 2.53: 352 2.53 - 3.13: 28705 3.13 - 3.72: 52282 3.72 - 4.31: 69432 4.31 - 4.90: 119396 Nonbonded interactions: 270167 Sorted by model distance: nonbonded pdb=" OG1 THR E 262 " pdb=" O3G ATP E 901 " model vdw 1.942 3.040 nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 1.953 3.040 nonbonded pdb=" O GLN K 262 " pdb=" OG SER K 265 " model vdw 1.953 3.040 nonbonded pdb=" OG1 THR F 458 " pdb=" OD1 ASP F 460 " model vdw 1.988 3.040 nonbonded pdb=" OG1 THR B 262 " pdb=" O3G ATP B 901 " model vdw 1.997 3.040 ... (remaining 270162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 91.720 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.070 ------------------------------------------------------------------------------- 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 : 0.006 0.887 34648 Z= 0.504 Angle : 0.548 10.715 46876 Z= 0.262 Chirality : 0.043 0.338 5269 Planarity : 0.003 0.038 6107 Dihedral : 11.257 142.777 13351 Min Nonbonded Distance : 1.942 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 Details of bonding type rmsd hydrogen bonds : bond 0.14818 ( 1586) hydrogen bonds : angle 5.47046 ( 4503) metal coordination : bond 0.08341 ( 8) metal coordination : angle 2.62217 ( 6) covalent geometry : bond 0.00318 (34638) covalent geometry : angle 0.54734 (46870) Misc. bond : bond 0.62969 ( 2) *********************** 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 to be fit. rotamer outliers: 69 poor density : 564 time to evaluate : 4.162 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: 0.6856 (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: 0.6732 (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: 0.5467 time to fit residues: 511.4720 Evaluate side-chains 325 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 300 time to evaluate : 4.141 ------------------------------------------------------------------------------- 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: 0.4980 chunk 323 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 129 optimal weight: 30.0000 chunk 203 optimal weight: 0.6980 chunk 249 optimal weight: 9.9990 chunk 387 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 C 206 ASN C 394 HIS D 225 GLN D 670 GLN E 337 GLN F 548 ASN G 344 HIS G 361 HIS G 362 GLN G 528 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.117657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.086864 restraints weight = 87235.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088754 restraints weight = 45861.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.090274 restraints weight = 29986.355| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 34648 Z= 0.199 Angle : 0.664 10.884 46876 Z= 0.326 Chirality : 0.045 0.203 5269 Planarity : 0.004 0.053 6107 Dihedral : 9.971 135.962 4969 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.24 % Favored : 94.74 % Rotamer: Outliers : 2.08 % Allowed : 9.19 % Favored : 88.73 % 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: 1.32 (0.13), residues: 4259 helix: 1.86 (0.12), residues: 2064 sheet: -0.47 (0.21), residues: 590 loop : 0.23 (0.17), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 486 HIS 0.008 0.001 HIS A 716 PHE 0.024 0.002 PHE A 141 TYR 0.016 0.002 TYR G 439 ARG 0.009 0.001 ARG E 672 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 1586) hydrogen bonds : angle 4.65891 ( 4503) metal coordination : bond 0.03018 ( 8) metal coordination : angle 4.05107 ( 6) covalent geometry : bond 0.00468 (34638) covalent geometry : angle 0.66231 (46870) Misc. bond : bond 0.00851 ( 2) *********************** 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 393 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 317 time to evaluate : 4.771 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: 0.6942 (ppp) cc_final: 0.5204 (mmt) REVERT: A 283 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8033 (tt0) REVERT: A 314 ASP cc_start: 0.8713 (t0) cc_final: 0.8480 (t0) REVERT: A 331 GLU cc_start: 0.6728 (pm20) cc_final: 0.6242 (pm20) REVERT: A 359 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7978 (mtm-85) REVERT: A 476 GLU cc_start: 0.7385 (pm20) cc_final: 0.7175 (pm20) REVERT: A 566 GLU cc_start: 0.7586 (mp0) cc_final: 0.7264 (mp0) REVERT: B 208 MET cc_start: 0.5731 (mmp) cc_final: 0.4987 (tpt) REVERT: B 285 MET cc_start: 0.8956 (mmm) cc_final: 0.8748 (mmt) REVERT: B 342 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8518 (mtm) REVERT: B 348 ARG cc_start: 0.8214 (ptp90) cc_final: 0.7929 (ptp90) REVERT: B 574 ASP cc_start: 0.8712 (m-30) cc_final: 0.8496 (t0) REVERT: B 773 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7469 (mm-30) REVERT: B 774 LEU cc_start: 0.8715 (tp) cc_final: 0.8442 (tp) REVERT: B 778 GLU cc_start: 0.8886 (tp30) cc_final: 0.8570 (pt0) REVERT: C 96 ARG cc_start: 0.6932 (tpm170) cc_final: 0.6577 (mtp-110) REVERT: C 253 MET cc_start: 0.8296 (mtp) cc_final: 0.7973 (mtp) REVERT: C 474 LEU cc_start: 0.8779 (mm) cc_final: 0.8458 (pt) REVERT: D 348 ARG cc_start: 0.7016 (ptt-90) cc_final: 0.6706 (ptt-90) REVERT: D 359 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7738 (mtm-85) REVERT: D 514 THR cc_start: 0.8562 (m) cc_final: 0.8333 (p) REVERT: D 556 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8129 (mp0) REVERT: E 314 ASP cc_start: 0.8965 (t0) cc_final: 0.8740 (t0) REVERT: E 378 ASP cc_start: 0.8227 (t0) cc_final: 0.7993 (t0) REVERT: E 556 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8272 (mt-10) REVERT: E 635 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7613 (mmm160) REVERT: E 689 THR cc_start: 0.8663 (p) cc_final: 0.8433 (p) REVERT: F 246 LYS cc_start: 0.8256 (tptp) cc_final: 0.7905 (tmtt) REVERT: F 315 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7761 (tp30) REVERT: G 187 SER cc_start: 0.7211 (t) cc_final: 0.6882 (m) REVERT: G 254 TYR cc_start: 0.7851 (t80) cc_final: 0.7417 (t80) REVERT: G 553 LYS cc_start: 0.7793 (ttmt) cc_final: 0.7582 (tttt) outliers start: 76 outliers final: 38 residues processed: 374 average time/residue: 0.6168 time to fit residues: 373.7479 Evaluate side-chains 320 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 6.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 665 SER 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 D residue 402 ASP Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain G residue 113 ILE 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 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 218 LYS 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 449 VAL Chi-restraints excluded: chain G residue 482 VAL 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 4 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 412 optimal weight: 0.5980 chunk 377 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 345 optimal weight: 0.9990 chunk 276 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 548 ASN B 651 GLN B 719 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS G 491 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.120701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090811 restraints weight = 86863.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092684 restraints weight = 44694.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094068 restraints weight = 30452.498| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34648 Z= 0.129 Angle : 0.595 11.228 46876 Z= 0.290 Chirality : 0.043 0.171 5269 Planarity : 0.004 0.051 6107 Dihedral : 9.399 136.448 4944 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.78 % Allowed : 10.53 % Favored : 87.69 % 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 (0.13), residues: 4259 helix: 1.82 (0.12), residues: 2064 sheet: -0.27 (0.21), residues: 585 loop : 0.22 (0.17), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 486 HIS 0.004 0.001 HIS A 716 PHE 0.014 0.001 PHE E 585 TYR 0.017 0.001 TYR G 439 ARG 0.025 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 1586) hydrogen bonds : angle 4.35243 ( 4503) metal coordination : bond 0.02246 ( 8) metal coordination : angle 4.04063 ( 6) covalent geometry : bond 0.00297 (34638) covalent geometry : angle 0.59313 (46870) Misc. bond : bond 0.00081 ( 2) *********************** 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 368 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 303 time to evaluate : 4.130 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: 0.6888 (ppp) cc_final: 0.5282 (mmt) REVERT: A 283 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7886 (tt0) REVERT: A 314 ASP cc_start: 0.8679 (t0) cc_final: 0.8465 (t0) REVERT: A 331 GLU cc_start: 0.6744 (pm20) cc_final: 0.6339 (pm20) REVERT: A 359 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.8014 (mtp-110) REVERT: A 476 GLU cc_start: 0.7288 (pm20) cc_final: 0.7039 (pm20) REVERT: B 208 MET cc_start: 0.5550 (mmp) cc_final: 0.4984 (tpt) REVERT: B 215 ASP cc_start: 0.9138 (t0) cc_final: 0.8880 (t0) REVERT: B 574 ASP cc_start: 0.8655 (m-30) cc_final: 0.8454 (t0) REVERT: B 773 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7360 (mm-30) REVERT: B 774 LEU cc_start: 0.8703 (tp) cc_final: 0.8433 (tp) REVERT: B 778 GLU cc_start: 0.8844 (tp30) cc_final: 0.8571 (pt0) REVERT: C 253 MET cc_start: 0.8262 (mtp) cc_final: 0.7947 (mtp) REVERT: C 474 LEU cc_start: 0.8739 (mm) cc_final: 0.8457 (pp) REVERT: D 208 MET cc_start: 0.6250 (ppp) cc_final: 0.5249 (tpt) REVERT: D 304 GLU cc_start: 0.8485 (tp30) cc_final: 0.8042 (mm-30) REVERT: D 514 THR cc_start: 0.8577 (m) cc_final: 0.8332 (p) REVERT: D 556 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8083 (mp0) REVERT: E 285 MET cc_start: 0.8608 (mmm) cc_final: 0.8341 (mmm) REVERT: E 314 ASP cc_start: 0.8931 (t0) cc_final: 0.8716 (t0) REVERT: E 556 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8269 (mt-10) REVERT: E 635 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7670 (mmm160) REVERT: E 752 TYR cc_start: 0.7068 (p90) cc_final: 0.6726 (p90) REVERT: F 223 MET cc_start: 0.8715 (tpp) cc_final: 0.8225 (tpp) REVERT: F 246 LYS cc_start: 0.8228 (tptp) cc_final: 0.7963 (tmtt) REVERT: F 315 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7729 (tp30) REVERT: F 325 LYS cc_start: 0.7731 (mmpt) cc_final: 0.7497 (mmmt) REVERT: F 762 MET cc_start: 0.8036 (ptm) cc_final: 0.7536 (ptm) REVERT: G 187 SER cc_start: 0.7001 (t) cc_final: 0.6763 (m) REVERT: G 242 SER cc_start: 0.8578 (m) cc_final: 0.7995 (t) REVERT: G 254 TYR cc_start: 0.7824 (t80) cc_final: 0.7355 (t80) REVERT: H 238 MET cc_start: 0.8271 (ttm) cc_final: 0.7812 (tpp) REVERT: J 158 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6970 (p0) outliers start: 65 outliers final: 38 residues processed: 349 average time/residue: 0.5127 time to fit residues: 291.6055 Evaluate side-chains 309 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN 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 635 ARG 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 211 TRP 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 504 LEU Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 286 optimal weight: 0.9990 chunk 393 optimal weight: 0.0000 chunk 34 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 384 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 351 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 716 HIS B 206 ASN F 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.119785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089468 restraints weight = 87110.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091487 restraints weight = 46260.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092428 restraints weight = 29880.174| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 34648 Z= 0.144 Angle : 0.587 12.170 46876 Z= 0.283 Chirality : 0.043 0.222 5269 Planarity : 0.004 0.052 6107 Dihedral : 9.057 137.732 4935 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.21 % Allowed : 10.97 % Favored : 86.82 % 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 (0.13), residues: 4259 helix: 1.76 (0.12), residues: 2069 sheet: -0.21 (0.21), residues: 589 loop : 0.21 (0.17), residues: 1601 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 0.027 0.001 PHE E 585 TYR 0.022 0.001 TYR K 259 ARG 0.011 0.000 ARG K 254 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 1586) hydrogen bonds : angle 4.22492 ( 4503) metal coordination : bond 0.02702 ( 8) metal coordination : angle 4.42397 ( 6) covalent geometry : bond 0.00336 (34638) covalent geometry : angle 0.58476 (46870) Misc. bond : bond 0.00091 ( 2) *********************** 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 369 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 4.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6954 (ppp) cc_final: 0.5224 (mmt) REVERT: A 314 ASP cc_start: 0.8723 (t0) cc_final: 0.8513 (t0) REVERT: A 331 GLU cc_start: 0.6729 (pm20) cc_final: 0.6276 (pm20) REVERT: A 359 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.8052 (mtp-110) REVERT: A 476 GLU cc_start: 0.7364 (pm20) cc_final: 0.7118 (pm20) REVERT: A 566 GLU cc_start: 0.7535 (mp0) cc_final: 0.7182 (mp0) REVERT: B 208 MET cc_start: 0.5792 (mmp) cc_final: 0.5324 (tpt) REVERT: B 215 ASP cc_start: 0.9159 (t0) cc_final: 0.8931 (t0) REVERT: B 556 GLU cc_start: 0.8652 (tp30) cc_final: 0.8361 (tp30) REVERT: B 574 ASP cc_start: 0.8659 (m-30) cc_final: 0.8456 (t0) REVERT: B 773 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7391 (mm-30) REVERT: B 774 LEU cc_start: 0.8688 (tp) cc_final: 0.8412 (tp) REVERT: B 778 GLU cc_start: 0.8864 (tp30) cc_final: 0.8493 (pt0) REVERT: C 253 MET cc_start: 0.8294 (mtp) cc_final: 0.7978 (mtp) REVERT: C 348 ARG cc_start: 0.6965 (tpp-160) cc_final: 0.6321 (ptp-170) REVERT: C 474 LEU cc_start: 0.8722 (mm) cc_final: 0.8385 (pp) REVERT: C 651 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: D 208 MET cc_start: 0.6159 (ppp) cc_final: 0.5955 (ppp) REVERT: D 304 GLU cc_start: 0.8491 (tp30) cc_final: 0.8048 (mm-30) REVERT: D 359 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.7754 (mtm-85) REVERT: D 514 THR cc_start: 0.8578 (m) cc_final: 0.8335 (p) REVERT: D 556 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8093 (mp0) REVERT: E 229 MET cc_start: 0.9198 (tpt) cc_final: 0.8641 (tpt) REVERT: E 254 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7879 (p90) REVERT: E 314 ASP cc_start: 0.8939 (t0) cc_final: 0.8698 (t0) REVERT: E 331 GLU cc_start: 0.8283 (mp0) cc_final: 0.8058 (mp0) REVERT: E 556 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8247 (mt-10) REVERT: E 635 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7715 (mmm160) REVERT: E 752 TYR cc_start: 0.7139 (p90) cc_final: 0.6797 (p90) REVERT: F 223 MET cc_start: 0.8723 (tpp) cc_final: 0.8231 (tpp) REVERT: F 246 LYS cc_start: 0.8210 (tptp) cc_final: 0.7963 (tmtt) REVERT: F 315 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7756 (tp30) REVERT: F 343 ASP cc_start: 0.8411 (m-30) cc_final: 0.8171 (m-30) REVERT: F 762 MET cc_start: 0.8014 (ptm) cc_final: 0.7453 (ptm) REVERT: G 187 SER cc_start: 0.7216 (t) cc_final: 0.6985 (m) REVERT: G 242 SER cc_start: 0.8486 (m) cc_final: 0.8014 (t) REVERT: G 539 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8283 (mt) REVERT: H 238 MET cc_start: 0.8294 (ttm) cc_final: 0.7771 (tpp) outliers start: 81 outliers final: 44 residues processed: 356 average time/residue: 0.4611 time to fit residues: 272.0074 Evaluate side-chains 317 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 269 time to evaluate : 4.165 ------------------------------------------------------------------------------- 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 342 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 335 VAL 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 635 ARG Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 211 TRP 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 482 VAL Chi-restraints excluded: chain G residue 539 LEU 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 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 J residue 166 THR 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 170 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 300 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 389 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 297 optimal weight: 0.7980 chunk 379 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.120647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090611 restraints weight = 86970.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093181 restraints weight = 43839.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.094187 restraints weight = 27148.945| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34648 Z= 0.115 Angle : 0.576 13.102 46876 Z= 0.275 Chirality : 0.042 0.232 5269 Planarity : 0.004 0.049 6107 Dihedral : 8.721 137.930 4929 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.11 % Allowed : 11.54 % Favored : 86.35 % 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 (0.13), residues: 4259 helix: 1.78 (0.12), residues: 2070 sheet: -0.07 (0.21), residues: 585 loop : 0.22 (0.17), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 486 HIS 0.004 0.001 HIS A 716 PHE 0.019 0.001 PHE E 585 TYR 0.018 0.001 TYR G 439 ARG 0.005 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 1586) hydrogen bonds : angle 4.11049 ( 4503) metal coordination : bond 0.02081 ( 8) metal coordination : angle 3.92525 ( 6) covalent geometry : bond 0.00259 (34638) covalent geometry : angle 0.57424 (46870) Misc. bond : bond 0.00087 ( 2) *********************** 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 361 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 284 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6972 (ppp) cc_final: 0.5215 (mmt) REVERT: A 202 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6108 (mt-10) REVERT: A 314 ASP cc_start: 0.8717 (t0) cc_final: 0.8497 (t0) REVERT: A 331 GLU cc_start: 0.6770 (pm20) cc_final: 0.6363 (pm20) REVERT: A 359 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.8049 (mtp-110) REVERT: A 398 MET cc_start: 0.9157 (mtp) cc_final: 0.8548 (mtp) REVERT: A 566 GLU cc_start: 0.7617 (mp0) cc_final: 0.7286 (mp0) REVERT: A 618 MET cc_start: 0.8910 (ttp) cc_final: 0.8684 (ttp) REVERT: B 208 MET cc_start: 0.5666 (mmp) cc_final: 0.5308 (tpt) REVERT: B 342 MET cc_start: 0.9065 (mtp) cc_final: 0.8248 (mtp) REVERT: B 348 ARG cc_start: 0.8154 (ptp90) cc_final: 0.7504 (ptp-170) REVERT: B 574 ASP cc_start: 0.8623 (m-30) cc_final: 0.8386 (t0) REVERT: B 773 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7306 (mm-30) REVERT: B 774 LEU cc_start: 0.8697 (tp) cc_final: 0.8425 (tp) REVERT: B 778 GLU cc_start: 0.8850 (tp30) cc_final: 0.8518 (pt0) REVERT: C 474 LEU cc_start: 0.8700 (mm) cc_final: 0.8322 (pp) REVERT: C 651 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: D 304 GLU cc_start: 0.8366 (tp30) cc_final: 0.7973 (mm-30) REVERT: D 342 MET cc_start: 0.9305 (tpp) cc_final: 0.9026 (tpp) REVERT: D 514 THR cc_start: 0.8580 (m) cc_final: 0.8350 (p) REVERT: D 556 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8046 (mp0) REVERT: E 223 MET cc_start: 0.8418 (tpp) cc_final: 0.8139 (mmm) REVERT: E 285 MET cc_start: 0.8605 (tpp) cc_final: 0.8030 (tpp) REVERT: E 314 ASP cc_start: 0.8929 (t0) cc_final: 0.8714 (t0) REVERT: E 331 GLU cc_start: 0.8233 (mp0) cc_final: 0.8013 (mp0) REVERT: E 332 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7515 (ttm-80) REVERT: E 342 MET cc_start: 0.8852 (mtp) cc_final: 0.8588 (mtp) REVERT: E 556 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8188 (mt-10) REVERT: E 752 TYR cc_start: 0.7089 (p90) cc_final: 0.6754 (p90) REVERT: F 246 LYS cc_start: 0.8133 (tptp) cc_final: 0.7926 (tmtt) REVERT: F 343 ASP cc_start: 0.8381 (m-30) cc_final: 0.8122 (m-30) REVERT: F 762 MET cc_start: 0.7933 (ptm) cc_final: 0.7447 (ptm) REVERT: F 785 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8024 (tptt) REVERT: G 242 SER cc_start: 0.8536 (m) cc_final: 0.7962 (t) REVERT: G 254 TYR cc_start: 0.7881 (t80) cc_final: 0.7475 (t80) REVERT: G 344 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.6983 (p90) outliers start: 77 outliers final: 46 residues processed: 344 average time/residue: 0.4473 time to fit residues: 254.0565 Evaluate side-chains 317 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 266 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 643 ILE 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 447 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL 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 F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL 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 211 TRP 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 482 VAL 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 307 LEU 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 166 THR Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 325 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 340 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 416 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN C 337 GLN ** C 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.117053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086608 restraints weight = 87679.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.088329 restraints weight = 46968.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.090261 restraints weight = 30447.702| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 34648 Z= 0.246 Angle : 0.669 13.453 46876 Z= 0.325 Chirality : 0.045 0.183 5269 Planarity : 0.004 0.051 6107 Dihedral : 8.767 140.566 4927 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.32 % Allowed : 12.06 % Favored : 85.62 % 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: 1.08 (0.13), residues: 4259 helix: 1.59 (0.12), residues: 2069 sheet: -0.32 (0.21), residues: 593 loop : 0.11 (0.17), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 486 HIS 0.012 0.001 HIS A 716 PHE 0.021 0.002 PHE G 169 TYR 0.020 0.002 TYR G 439 ARG 0.009 0.000 ARG A 717 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 1586) hydrogen bonds : angle 4.36513 ( 4503) metal coordination : bond 0.03660 ( 8) metal coordination : angle 6.29275 ( 6) covalent geometry : bond 0.00582 (34638) covalent geometry : angle 0.66488 (46870) Misc. bond : bond 0.00077 ( 2) *********************** 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 359 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 274 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7230 (ppp) cc_final: 0.5459 (mmt) REVERT: A 359 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.8045 (mtp-110) REVERT: A 566 GLU cc_start: 0.7670 (mp0) cc_final: 0.7468 (mp0) REVERT: B 293 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: B 342 MET cc_start: 0.9112 (mtp) cc_final: 0.8407 (mtp) REVERT: B 574 ASP cc_start: 0.8715 (m-30) cc_final: 0.8502 (t0) REVERT: B 773 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7259 (mm-30) REVERT: B 774 LEU cc_start: 0.8723 (tp) cc_final: 0.8440 (tp) REVERT: B 778 GLU cc_start: 0.8803 (tp30) cc_final: 0.8477 (pt0) REVERT: C 253 MET cc_start: 0.8266 (mtp) cc_final: 0.7991 (mtp) REVERT: C 427 GLU cc_start: 0.8035 (tp30) cc_final: 0.7749 (tp30) REVERT: C 474 LEU cc_start: 0.8743 (mm) cc_final: 0.8386 (pp) REVERT: C 651 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: D 208 MET cc_start: 0.6244 (ppp) cc_final: 0.5279 (tpt) REVERT: D 359 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.7718 (mtm-85) REVERT: D 514 THR cc_start: 0.8636 (m) cc_final: 0.8391 (p) REVERT: D 556 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8100 (mp0) REVERT: E 254 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7790 (p90) REVERT: E 314 ASP cc_start: 0.8975 (t0) cc_final: 0.8742 (t0) REVERT: E 331 GLU cc_start: 0.8193 (mp0) cc_final: 0.7971 (mp0) REVERT: E 332 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7609 (ttm-80) REVERT: E 556 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8248 (mt-10) REVERT: E 617 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: E 635 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7765 (mmm160) REVERT: E 752 TYR cc_start: 0.7255 (p90) cc_final: 0.6896 (p90) REVERT: F 246 LYS cc_start: 0.8290 (tptp) cc_final: 0.8048 (tmtt) REVERT: F 785 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8105 (tptp) REVERT: G 378 SER cc_start: 0.7842 (t) cc_final: 0.7491 (p) REVERT: H 281 MET cc_start: 0.2262 (mmp) cc_final: 0.1936 (mmp) outliers start: 85 outliers final: 50 residues processed: 344 average time/residue: 0.4466 time to fit residues: 252.9472 Evaluate side-chains 320 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 263 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 639 ILE 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 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 617 GLU Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL 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 211 TRP 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 495 MET Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 561 LEU 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 307 LEU 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 J residue 166 THR Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 312 optimal weight: 2.9990 chunk 399 optimal weight: 0.4980 chunk 244 optimal weight: 0.1980 chunk 359 optimal weight: 3.9990 chunk 402 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 409 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** C 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.088917 restraints weight = 87173.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091243 restraints weight = 43946.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.092190 restraints weight = 27599.579| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34648 Z= 0.139 Angle : 0.593 15.586 46876 Z= 0.285 Chirality : 0.042 0.161 5269 Planarity : 0.004 0.045 6107 Dihedral : 8.564 140.193 4927 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.84 % Favored : 95.14 % Rotamer: Outliers : 1.94 % Allowed : 12.72 % Favored : 85.34 % 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: 1.17 (0.13), residues: 4259 helix: 1.65 (0.12), residues: 2071 sheet: -0.19 (0.21), residues: 584 loop : 0.14 (0.17), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 486 HIS 0.003 0.001 HIS G 139 PHE 0.012 0.001 PHE G 260 TYR 0.018 0.001 TYR G 439 ARG 0.006 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 1586) hydrogen bonds : angle 4.15580 ( 4503) metal coordination : bond 0.02166 ( 8) metal coordination : angle 5.24871 ( 6) covalent geometry : bond 0.00322 (34638) covalent geometry : angle 0.59045 (46870) Misc. bond : bond 0.00076 ( 2) *********************** 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 359 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 4.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7174 (ppp) cc_final: 0.5365 (mmt) REVERT: A 359 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8076 (mtp-110) REVERT: A 398 MET cc_start: 0.9190 (mtp) cc_final: 0.8702 (mtp) REVERT: B 208 MET cc_start: 0.5635 (mmp) cc_final: 0.5397 (tpt) REVERT: B 293 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: B 342 MET cc_start: 0.9078 (mtp) cc_final: 0.8305 (mtp) REVERT: B 348 ARG cc_start: 0.8121 (ptp90) cc_final: 0.7504 (ptt180) REVERT: B 432 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8588 (tm-30) REVERT: B 773 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7332 (mm-30) REVERT: B 774 LEU cc_start: 0.8701 (tp) cc_final: 0.8415 (tp) REVERT: B 778 GLU cc_start: 0.8849 (tp30) cc_final: 0.8507 (pt0) REVERT: C 427 GLU cc_start: 0.8061 (tp30) cc_final: 0.7780 (tp30) REVERT: C 474 LEU cc_start: 0.8706 (mm) cc_final: 0.8321 (pp) REVERT: C 651 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: D 208 MET cc_start: 0.6264 (ppp) cc_final: 0.5281 (tpt) REVERT: D 359 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.7733 (mtm-85) REVERT: D 556 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8090 (mp0) REVERT: D 784 MET cc_start: 0.8612 (mmm) cc_final: 0.8207 (mmm) REVERT: E 223 MET cc_start: 0.8565 (tpp) cc_final: 0.8304 (mmm) REVERT: E 254 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.7975 (p90) REVERT: E 314 ASP cc_start: 0.8916 (t0) cc_final: 0.8685 (t0) REVERT: E 331 GLU cc_start: 0.8153 (mp0) cc_final: 0.7873 (mp0) REVERT: E 332 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7487 (ttm-80) REVERT: E 556 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8243 (mt-10) REVERT: E 617 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: E 752 TYR cc_start: 0.7166 (p90) cc_final: 0.6822 (p90) REVERT: F 246 LYS cc_start: 0.8217 (tptp) cc_final: 0.7984 (tmtt) REVERT: F 785 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8082 (tptp) REVERT: G 122 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8101 (mm) REVERT: G 242 SER cc_start: 0.8482 (m) cc_final: 0.7993 (t) REVERT: G 344 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.6865 (p90) REVERT: G 378 SER cc_start: 0.7724 (t) cc_final: 0.7467 (p) REVERT: G 440 MET cc_start: 0.8578 (ttt) cc_final: 0.8376 (mtt) REVERT: H 281 MET cc_start: 0.2205 (mmp) cc_final: 0.1863 (mmp) outliers start: 71 outliers final: 49 residues processed: 349 average time/residue: 0.4649 time to fit residues: 267.3604 Evaluate side-chains 324 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 643 ILE 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 424 LEU Chi-restraints excluded: chain B residue 432 GLN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 402 ASP 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 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 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 617 GLU Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP 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 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 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 166 THR Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 324 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 328 optimal weight: 0.9990 chunk 344 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN C 719 HIS ** C 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN G 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.117844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087416 restraints weight = 87107.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089706 restraints weight = 44339.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090747 restraints weight = 28530.628| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 34648 Z= 0.209 Angle : 0.641 15.775 46876 Z= 0.310 Chirality : 0.044 0.159 5269 Planarity : 0.004 0.048 6107 Dihedral : 8.595 141.327 4927 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 2.19 % Allowed : 12.96 % Favored : 84.85 % 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: 1.05 (0.13), residues: 4259 helix: 1.57 (0.12), residues: 2069 sheet: -0.25 (0.21), residues: 589 loop : 0.06 (0.17), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 486 HIS 0.004 0.001 HIS E 394 PHE 0.017 0.002 PHE G 169 TYR 0.019 0.001 TYR G 439 ARG 0.006 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1586) hydrogen bonds : angle 4.26814 ( 4503) metal coordination : bond 0.02958 ( 8) metal coordination : angle 6.20590 ( 6) covalent geometry : bond 0.00496 (34638) covalent geometry : angle 0.63740 (46870) Misc. bond : bond 0.00076 ( 2) *********************** 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 347 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 267 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7194 (ppp) cc_final: 0.5348 (mmt) REVERT: B 293 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: B 342 MET cc_start: 0.9064 (mtp) cc_final: 0.8359 (mtp) REVERT: B 348 ARG cc_start: 0.8205 (ptp90) cc_final: 0.7837 (ptp-170) REVERT: B 773 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7323 (mm-30) REVERT: B 774 LEU cc_start: 0.8716 (tp) cc_final: 0.8427 (tp) REVERT: B 778 GLU cc_start: 0.8825 (tp30) cc_final: 0.8455 (pt0) REVERT: C 427 GLU cc_start: 0.8045 (tp30) cc_final: 0.7768 (tp30) REVERT: C 474 LEU cc_start: 0.8754 (mm) cc_final: 0.8366 (pp) REVERT: C 651 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: D 342 MET cc_start: 0.9350 (tpp) cc_final: 0.9124 (tpp) REVERT: D 359 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.7757 (mtm-85) REVERT: D 556 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8090 (mp0) REVERT: D 784 MET cc_start: 0.8617 (mmm) cc_final: 0.8251 (mmm) REVERT: E 223 MET cc_start: 0.8579 (tpp) cc_final: 0.8334 (mmm) REVERT: E 254 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7863 (p90) REVERT: E 314 ASP cc_start: 0.8960 (t0) cc_final: 0.8721 (t0) REVERT: E 331 GLU cc_start: 0.8145 (mp0) cc_final: 0.7843 (mp0) REVERT: E 332 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7504 (ttm-80) REVERT: E 556 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8243 (mt-10) REVERT: E 617 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: E 635 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7708 (mmm160) REVERT: F 246 LYS cc_start: 0.8277 (tptp) cc_final: 0.8008 (tmtt) REVERT: F 785 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (tptp) REVERT: G 122 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8113 (mm) REVERT: G 242 SER cc_start: 0.8518 (m) cc_final: 0.7952 (t) REVERT: G 344 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7523 (p90) REVERT: G 378 SER cc_start: 0.7881 (t) cc_final: 0.7615 (p) REVERT: H 281 MET cc_start: 0.2204 (mmp) cc_final: 0.1859 (mmp) outliers start: 80 outliers final: 59 residues processed: 331 average time/residue: 0.4628 time to fit residues: 253.7214 Evaluate side-chains 328 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 643 ILE 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 319 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 402 ASP 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 782 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL 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 617 GLU Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP 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 479 SER Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 561 LEU 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 307 LEU 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 156 LEU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 53 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 314 optimal weight: 0.7980 chunk 295 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 390 optimal weight: 0.7980 chunk 330 optimal weight: 9.9990 chunk 399 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 HIS G 478 ASN ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.116503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086411 restraints weight = 87873.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.087791 restraints weight = 48287.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.089461 restraints weight = 31754.135| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 34648 Z= 0.270 Angle : 0.701 16.104 46876 Z= 0.342 Chirality : 0.045 0.177 5269 Planarity : 0.004 0.047 6107 Dihedral : 8.766 142.823 4927 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.87 % Favored : 94.11 % Rotamer: Outliers : 2.24 % Allowed : 13.07 % Favored : 84.69 % 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: 0.80 (0.13), residues: 4259 helix: 1.39 (0.12), residues: 2072 sheet: -0.44 (0.21), residues: 596 loop : -0.08 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 486 HIS 0.013 0.001 HIS C 719 PHE 0.022 0.002 PHE G 169 TYR 0.025 0.002 TYR G 399 ARG 0.007 0.001 ARG C 717 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1586) hydrogen bonds : angle 4.44642 ( 4503) metal coordination : bond 0.01893 ( 8) metal coordination : angle 6.76074 ( 6) covalent geometry : bond 0.00638 (34638) covalent geometry : angle 0.69662 (46870) Misc. bond : bond 0.00081 ( 2) *********************** 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 341 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 259 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7233 (ppp) cc_final: 0.5415 (mmt) REVERT: B 208 MET cc_start: 0.5328 (mmp) cc_final: 0.4866 (ttt) REVERT: B 293 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: B 342 MET cc_start: 0.9099 (mtp) cc_final: 0.8394 (mtp) REVERT: B 348 ARG cc_start: 0.8205 (ptp90) cc_final: 0.7955 (ptp-170) REVERT: B 773 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7384 (mm-30) REVERT: B 774 LEU cc_start: 0.8726 (tp) cc_final: 0.8431 (tp) REVERT: B 778 GLU cc_start: 0.8844 (tp30) cc_final: 0.8455 (pt0) REVERT: C 253 MET cc_start: 0.8308 (mtp) cc_final: 0.8012 (mtp) REVERT: C 427 GLU cc_start: 0.8043 (tp30) cc_final: 0.7782 (tp30) REVERT: C 474 LEU cc_start: 0.8746 (mm) cc_final: 0.8393 (pp) REVERT: C 499 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8464 (mm) REVERT: C 651 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8054 (mp10) REVERT: D 359 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.7796 (mtm-85) REVERT: D 556 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8094 (mp0) REVERT: E 223 MET cc_start: 0.8632 (tpp) cc_final: 0.8390 (mmm) REVERT: E 254 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.7725 (p90) REVERT: E 314 ASP cc_start: 0.8988 (t0) cc_final: 0.8697 (t0) REVERT: E 331 GLU cc_start: 0.8147 (mp0) cc_final: 0.7833 (mp0) REVERT: E 332 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7567 (ttm-80) REVERT: E 556 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8224 (mt-10) REVERT: F 246 LYS cc_start: 0.8304 (tptp) cc_final: 0.8040 (tmtt) REVERT: F 762 MET cc_start: 0.8326 (tmm) cc_final: 0.8039 (ttp) REVERT: F 785 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7988 (tppt) REVERT: G 122 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8158 (mm) REVERT: G 378 SER cc_start: 0.8058 (t) cc_final: 0.7803 (p) REVERT: H 281 MET cc_start: 0.2286 (mmp) cc_final: 0.1949 (mmp) outliers start: 82 outliers final: 60 residues processed: 325 average time/residue: 0.4498 time to fit residues: 242.9326 Evaluate side-chains 322 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 255 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 643 ILE 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 319 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 402 ASP 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 782 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL 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 560 MET Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP 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 479 SER Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 561 LEU 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 307 LEU 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 166 THR Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 199 optimal weight: 6.9990 chunk 169 optimal weight: 0.3980 chunk 264 optimal weight: 2.9990 chunk 317 optimal weight: 0.6980 chunk 128 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 367 optimal weight: 0.2980 chunk 219 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.118334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088472 restraints weight = 86881.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.089899 restraints weight = 46643.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092101 restraints weight = 30904.163| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34648 Z= 0.140 Angle : 0.622 17.215 46876 Z= 0.297 Chirality : 0.043 0.147 5269 Planarity : 0.004 0.045 6107 Dihedral : 8.586 142.132 4927 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 1.86 % Allowed : 13.37 % Favored : 84.77 % 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: 0.96 (0.13), residues: 4259 helix: 1.50 (0.12), residues: 2073 sheet: -0.32 (0.21), residues: 595 loop : 0.02 (0.17), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 486 HIS 0.020 0.001 HIS C 719 PHE 0.022 0.001 PHE D 373 TYR 0.021 0.001 TYR G 399 ARG 0.005 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 1586) hydrogen bonds : angle 4.19915 ( 4503) metal coordination : bond 0.00781 ( 8) metal coordination : angle 5.38438 ( 6) covalent geometry : bond 0.00326 (34638) covalent geometry : angle 0.61932 (46870) Misc. bond : bond 0.00076 ( 2) ********************** 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 337 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 4.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7206 (ppp) cc_final: 0.5388 (mmt) REVERT: A 359 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.8073 (mtp-110) REVERT: B 208 MET cc_start: 0.5412 (mmp) cc_final: 0.4863 (ttt) REVERT: B 293 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: B 342 MET cc_start: 0.9061 (mtp) cc_final: 0.8231 (mtp) REVERT: B 348 ARG cc_start: 0.8207 (ptp90) cc_final: 0.7978 (ptp-170) REVERT: B 628 PHE cc_start: 0.7826 (m-80) cc_final: 0.7542 (m-80) REVERT: B 773 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7285 (mm-30) REVERT: B 774 LEU cc_start: 0.8710 (tp) cc_final: 0.8417 (tp) REVERT: B 778 GLU cc_start: 0.8803 (tp30) cc_final: 0.8449 (pt0) REVERT: C 168 MET cc_start: 0.6518 (ppp) cc_final: 0.6027 (ppp) REVERT: C 427 GLU cc_start: 0.8033 (tp30) cc_final: 0.7770 (tp30) REVERT: C 474 LEU cc_start: 0.8760 (mm) cc_final: 0.8385 (pp) REVERT: C 499 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8428 (mm) REVERT: C 651 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: D 208 MET cc_start: 0.6126 (ppp) cc_final: 0.5160 (tpp) REVERT: D 359 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.7826 (mtm-85) REVERT: D 556 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8060 (mp0) REVERT: E 223 MET cc_start: 0.8589 (tpp) cc_final: 0.8350 (mmm) REVERT: E 254 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.7950 (p90) REVERT: E 314 ASP cc_start: 0.8912 (t0) cc_final: 0.8665 (t0) REVERT: E 331 GLU cc_start: 0.8126 (mp0) cc_final: 0.7856 (mp0) REVERT: E 332 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7589 (ttm-80) REVERT: E 556 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8269 (mt-10) REVERT: F 719 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6067 (t70) REVERT: F 762 MET cc_start: 0.8334 (tmm) cc_final: 0.8073 (ttp) REVERT: F 785 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8087 (tptp) REVERT: G 122 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8145 (mm) REVERT: G 242 SER cc_start: 0.8500 (m) cc_final: 0.7958 (t) REVERT: G 344 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.6883 (p90) REVERT: G 378 SER cc_start: 0.7978 (t) cc_final: 0.7744 (p) REVERT: G 422 MET cc_start: 0.8643 (tpp) cc_final: 0.8132 (mmm) REVERT: H 281 MET cc_start: 0.2270 (mmp) cc_final: 0.1924 (mmp) outliers start: 68 outliers final: 52 residues processed: 325 average time/residue: 0.4669 time to fit residues: 252.4656 Evaluate side-chains 324 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 643 ILE 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 319 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 402 ASP 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 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 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 F residue 404 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 LYS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP 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 383 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 561 LEU 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 307 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 123 optimal weight: 8.9990 chunk 352 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 426 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 388 optimal weight: 0.0370 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.117813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087497 restraints weight = 87175.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.089759 restraints weight = 44427.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.090853 restraints weight = 28365.490| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34648 Z= 0.184 Angle : 0.643 16.626 46876 Z= 0.309 Chirality : 0.043 0.144 5269 Planarity : 0.004 0.046 6107 Dihedral : 8.575 142.078 4927 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.47 % Favored : 94.51 % Rotamer: Outliers : 1.89 % Allowed : 13.48 % Favored : 84.63 % 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: 0.92 (0.13), residues: 4259 helix: 1.48 (0.12), residues: 2070 sheet: -0.35 (0.21), residues: 594 loop : -0.03 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 486 HIS 0.004 0.001 HIS G 208 PHE 0.018 0.002 PHE G 340 TYR 0.021 0.001 TYR G 445 ARG 0.005 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 1586) hydrogen bonds : angle 4.24639 ( 4503) metal coordination : bond 0.01014 ( 8) metal coordination : angle 4.95316 ( 6) covalent geometry : bond 0.00437 (34638) covalent geometry : angle 0.64069 (46870) Misc. bond : bond 0.00078 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12606.85 seconds wall clock time: 224 minutes 1.15 seconds (13441.15 seconds total)