Starting phenix.real_space_refine on Sun Jun 29 23:04:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dat_27275/06_2025/8dat_27275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dat_27275/06_2025/8dat_27275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dat_27275/06_2025/8dat_27275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dat_27275/06_2025/8dat_27275.map" model { file = "/net/cci-nas-00/data/ceres_data/8dat_27275/06_2025/8dat_27275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dat_27275/06_2025/8dat_27275.cif" } resolution = 3.8 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= -0.022 sd= 1.089 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 157 5.16 5 C 21678 2.51 5 N 6018 2.21 5 O 6751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34635 Number of models: 1 Model: "" Number of chains: 18 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: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4361 Classifications: {'peptide': 561} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 531} 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: "L" 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 28493 SG CYS G 137 46.570 46.552 94.504 1.00 85.59 S ATOM 28553 SG CYS G 145 50.237 47.200 94.103 1.00 76.33 S ATOM 28580 SG CYS G 148 48.689 46.859 97.510 1.00 77.07 S ATOM 29050 SG CYS G 204 76.186 88.657 113.339 1.00100.27 S ATOM 29148 SG CYS G 216 76.282 90.588 110.164 1.00 82.25 S ATOM 29169 SG CYS G 219 73.577 91.235 112.527 1.00 80.75 S Time building chain proxies: 19.51, per 1000 atoms: 0.56 Number of scatterers: 34635 At special positions: 0 Unit cell: (151.088, 167.048, 190.456, 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 157 16.00 P 29 15.00 O 6751 8.00 N 6018 7.00 C 21678 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: 9.91 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8210 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 25 sheets defined 52.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 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: 4.003A pdb=" N GLU A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 4.006A pdb=" N LYS A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 220 through 236 removed outlier: 3.521A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.333A 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: 3.790A 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 320 removed outlier: 4.131A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 4.141A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 4.047A 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 468 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 492 through 509 removed outlier: 4.275A 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: 4.098A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 546 removed outlier: 3.763A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 562 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 588 through 592 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: 3.625A pdb=" N PHE A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 764 " --> pdb=" O GLU A 760 " (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: 4.092A 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: 3.810A 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 281 through 286 Processing helix chain 'B' and resid 293 through 306 Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.207A pdb=" N ILE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 removed outlier: 3.979A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.631A 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 454 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: 4.496A 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: 3.787A 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 589 through 592 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 671 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 763 removed outlier: 3.613A pdb=" N PHE B 758 " --> pdb=" O THR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 787 Processing helix chain 'C' and resid 52 through 60 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: 4.216A pdb=" N LYS C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Proline residue: C 147 - end of helix Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.790A 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: 4.596A 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 removed outlier: 3.539A pdb=" N LYS C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.604A 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 315 through 319 Processing helix chain 'C' and resid 328 through 345 removed outlier: 3.927A pdb=" N VAL C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 4.316A 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 Processing helix chain 'C' and resid 417 through 437 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.582A pdb=" N GLU C 476 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 removed outlier: 4.721A 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: 3.680A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.618A 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: 3.583A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 764 " --> pdb=" O GLU C 760 " (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: 3.637A pdb=" N ILE D 216 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 236 removed outlier: 4.125A 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 286 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: 4.238A 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: 4.039A 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: 3.938A pdb=" N TYR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.600A 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 620 Processing helix chain 'D' and resid 640 through 645 removed outlier: 3.533A pdb=" N ARG D 645 " --> pdb=" O ALA D 642 " (cutoff:3.500A) 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: 3.757A 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: 4.210A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 237 through 244 removed outlier: 3.687A pdb=" N LYS E 241 " --> pdb=" O PRO E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 287 removed outlier: 3.632A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 305 Processing helix chain 'E' and resid 315 through 320 removed outlier: 4.016A pdb=" N ILE E 319 " --> pdb=" O GLU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.914A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.232A 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 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 448 through 454 Processing helix chain 'E' and resid 458 through 469 Processing helix chain 'E' and resid 472 through 476 removed outlier: 3.625A pdb=" N GLU E 476 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 509 removed outlier: 4.211A 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: 3.729A pdb=" N TYR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 removed outlier: 3.537A pdb=" N VAL E 545 " --> pdb=" O VAL E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 568 through 579 Processing helix chain 'E' and resid 588 through 592 Processing helix chain 'E' and resid 609 through 620 Processing helix chain 'E' and resid 635 through 639 Processing helix chain 'E' and resid 640 through 645 Processing helix chain 'E' and resid 659 through 671 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: 3.679A pdb=" N PHE E 758 " --> pdb=" O THR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 787 Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 236 removed outlier: 4.655A pdb=" N LEU F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 237 through 244 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 291 through 306 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 326 Processing helix chain 'F' and resid 328 through 345 removed outlier: 3.581A pdb=" N ARG F 332 " --> pdb=" O GLY F 328 " (cutoff:3.500A) 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: 3.624A 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 Processing helix chain 'F' and resid 492 through 509 removed outlier: 4.030A 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: 4.055A 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 562 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 removed outlier: 3.575A pdb=" N ARG F 645 " --> pdb=" O ALA F 642 " (cutoff:3.500A) 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 788 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.647A 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 241 through 256 removed outlier: 4.327A pdb=" N ILE G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.820A 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 411 removed outlier: 4.097A pdb=" N THR G 410 " --> pdb=" O GLU G 406 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA G 411 " --> pdb=" O ALA G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 508 Processing helix chain 'G' and resid 509 through 515 removed outlier: 3.750A pdb=" N SER G 514 " --> pdb=" O ASN G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 525 removed outlier: 4.133A pdb=" N GLU G 522 " --> pdb=" O ASN G 518 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 523 " --> pdb=" O LEU G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 537 removed outlier: 3.711A 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 Processing helix chain 'H' and resid 243 through 253 Processing helix chain 'J' and resid 122 through 135 removed outlier: 3.905A pdb=" N VAL J 126 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 160 removed outlier: 4.421A pdb=" N TYR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 235 removed outlier: 3.797A pdb=" N VAL K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 260 Processing helix chain 'L' and resid 322 through 335 removed outlier: 3.763A pdb=" N VAL L 326 " --> pdb=" O THR L 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 removed outlier: 7.735A pdb=" N CYS A 92 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU A 37 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 94 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP A 39 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 110 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 36 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 6.841A pdb=" N LYS A 119 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 166 removed outlier: 6.085A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 278 removed outlier: 3.550A pdb=" N VAL A 352 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 356 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 251 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR A 357 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET A 253 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 252 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 548 through 552 removed outlier: 6.933A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A 582 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 630 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 584 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA A 632 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 586 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.350A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE G 215 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 278 " --> pdb=" O ILE G 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 548 through 552 removed outlier: 6.632A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP B 587 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 552 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AA9, 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: 5.768A pdb=" N VAL C 175 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU C 127 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 124 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.088A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 356 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 548 through 552 removed outlier: 7.074A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 525 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 275 through 280 removed outlier: 6.818A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 479 through 480 removed outlier: 3.830A pdb=" N PHE D 549 " --> pdb=" O GLU D 480 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLY D 523 " --> pdb=" O GLN D 651 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE D 653 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU D 525 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 312 through 314 removed outlier: 3.693A pdb=" N ARG E 375 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 479 through 480 Processing sheet with id=AB8, first strand: chain 'F' and resid 275 through 280 removed outlier: 6.954A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY F 250 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL F 377 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 548 through 552 removed outlier: 6.825A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 224 through 226 removed outlier: 6.027A pdb=" N ILE G 224 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET G 440 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU G 226 " --> pdb=" O MET G 440 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N SER G 442 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 236 through 239 removed outlier: 3.939A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE G 396 " --> pdb=" O HIS G 468 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS G 468 " --> pdb=" O ILE G 396 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER G 398 " --> pdb=" O LEU G 466 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 466 " --> pdb=" O SER G 398 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 290 through 291 Processing sheet with id=AC4, first strand: chain 'G' and resid 415 through 416 removed outlier: 3.543A 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 115 removed outlier: 6.624A pdb=" N PHE J 104 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU J 169 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS J 106 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N LEU J 171 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 212 through 216 removed outlier: 3.935A pdb=" N SER K 265 " --> pdb=" O GLN K 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 312 through 316 removed outlier: 4.230A pdb=" N SER L 365 " --> pdb=" O GLN L 302 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU L 343 " --> pdb=" O LEU L 350 " (cutoff:3.500A) 1622 hydrogen bonds defined for protein. 4602 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: 13.73 Time building geometry restraints manager: 11.22 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: 11722 1.34 - 1.46: 6664 1.46 - 1.58: 16497 1.58 - 1.69: 46 1.69 - 1.81: 290 Bond restraints: 35219 Sorted by residual: bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+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 2.97e+01 bond pdb=" C5 ADP A 902 " pdb=" C6 ADP A 902 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.82e+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 1.82e+01 ... (remaining 35214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 47224 2.30 - 4.60: 342 4.60 - 6.89: 63 6.89 - 9.19: 14 9.19 - 11.49: 8 Bond angle restraints: 47651 Sorted by residual: angle pdb=" N ILE F 592 " pdb=" CA ILE F 592 " pdb=" C ILE F 592 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" CA THR B 24 " pdb=" C THR B 24 " pdb=" O THR B 24 " ideal model delta sigma weight residual 122.36 117.61 4.75 1.21e+00 6.83e-01 1.54e+01 angle pdb=" PA ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sigma weight residual 120.50 131.99 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA ARG C 235 " pdb=" C ARG C 235 " pdb=" O ARG C 235 " ideal model delta sigma weight residual 120.42 117.03 3.39 1.06e+00 8.90e-01 1.02e+01 angle pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " pdb=" C4' ADP A 902 " ideal model delta sigma weight residual 111.00 101.49 9.51 3.00e+00 1.11e-01 1.01e+01 ... (remaining 47646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 21521 34.25 - 68.50: 242 68.50 - 102.75: 14 102.75 - 137.00: 9 137.00 - 171.26: 2 Dihedral angle restraints: 21788 sinusoidal: 9108 harmonic: 12680 Sorted by residual: dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 111.26 -171.26 1 2.00e+01 2.50e-03 4.77e+01 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 -120.81 -147.64 1 2.00e+01 2.50e-03 4.43e+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 -132.68 -135.77 1 2.00e+01 2.50e-03 4.12e+01 ... (remaining 21785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4829 0.070 - 0.139: 509 0.139 - 0.209: 10 0.209 - 0.278: 7 0.278 - 0.348: 9 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ASN G 510 " pdb=" N ASN G 510 " pdb=" C ASN G 510 " pdb=" CB ASN G 510 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C2' ATP E 901 " pdb=" C1' ATP E 901 " pdb=" C3' ATP E 901 " pdb=" O2' ATP E 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP B 901 " pdb=" C1' ATP B 901 " pdb=" C3' ATP B 901 " pdb=" O2' ATP B 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 5361 not shown) Planarity restraints: 6206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 505 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO E 506 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 506 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 506 " -0.022 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 1.46e-02 2.13e+00 pdb=" C LEU C 234 " 0.025 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=" C GLY B 554 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 555 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 555 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 555 " -0.020 5.00e-02 4.00e+02 ... (remaining 6203 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 372 2.55 - 3.13: 29897 3.13 - 3.72: 53278 3.72 - 4.31: 70418 4.31 - 4.90: 120627 Nonbonded interactions: 274592 Sorted by model distance: nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 1.958 3.040 nonbonded pdb=" OG1 THR E 262 " pdb=" O3G ATP E 901 " model vdw 1.963 3.040 nonbonded pdb=" OG1 THR B 262 " pdb=" O3G ATP B 901 " model vdw 1.977 3.040 nonbonded pdb=" OG SER G 351 " pdb=" OE2 GLU G 354 " model vdw 1.982 3.040 nonbonded pdb=" OG1 THR F 458 " pdb=" OD1 ASP F 460 " model vdw 1.995 3.040 ... (remaining 274587 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) selection = (chain 'L' and resid 301 through 373) } 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: 3.490 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: 0.020 Extract box with map and model: 1.450 Check model and map are aligned: 0.270 Set scattering table: 0.300 Process input model: 84.590 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 35229 Z= 0.155 Angle : 0.527 11.489 47657 Z= 0.250 Chirality : 0.043 0.348 5364 Planarity : 0.003 0.040 6206 Dihedral : 11.089 171.256 13578 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer: Outliers : 1.34 % Allowed : 4.62 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.81 (0.14), residues: 4330 helix: 2.38 (0.12), residues: 2065 sheet: -0.13 (0.21), residues: 615 loop : 0.32 (0.17), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 561 HIS 0.002 0.001 HIS G 528 PHE 0.009 0.001 PHE G 527 TYR 0.010 0.001 TYR B 254 ARG 0.002 0.000 ARG K 272 Details of bonding type rmsd hydrogen bonds : bond 0.14842 ( 1622) hydrogen bonds : angle 5.62006 ( 4602) metal coordination : bond 0.06280 ( 8) metal coordination : angle 2.52194 ( 6) covalent geometry : bond 0.00286 (35219) covalent geometry : angle 0.52663 (47651) Misc. bond : bond 0.08651 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 492 time to evaluate : 4.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 TYR cc_start: 0.6902 (m-80) cc_final: 0.6682 (m-10) REVERT: A 161 HIS cc_start: 0.6251 (m90) cc_final: 0.5967 (m-70) REVERT: A 173 PHE cc_start: 0.7196 (m-80) cc_final: 0.6187 (m-80) REVERT: A 223 MET cc_start: 0.8727 (mmm) cc_final: 0.8389 (mmm) REVERT: A 283 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 302 GLU cc_start: 0.8854 (tt0) cc_final: 0.8651 (mt-10) REVERT: B 283 GLU cc_start: 0.7317 (tt0) cc_final: 0.7109 (tt0) REVERT: B 504 GLU cc_start: 0.8652 (tt0) cc_final: 0.8266 (mm-30) REVERT: B 571 ASP cc_start: 0.8347 (t0) cc_final: 0.8073 (t0) REVERT: C 345 MET cc_start: 0.8054 (ptp) cc_final: 0.7749 (ptt) REVERT: C 571 ASP cc_start: 0.8588 (t0) cc_final: 0.8377 (t0) REVERT: D 301 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 493 ASP cc_start: 0.8206 (m-30) cc_final: 0.7606 (t70) REVERT: D 522 LYS cc_start: 0.8471 (tttt) cc_final: 0.8214 (tptm) REVERT: D 628 PHE cc_start: 0.8315 (m-80) cc_final: 0.7968 (m-10) REVERT: E 315 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8438 (mt-10) REVERT: E 346 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7750 (ptmt) REVERT: E 440 ILE cc_start: 0.7487 (mt) cc_final: 0.7285 (tt) REVERT: F 253 MET cc_start: 0.8321 (mtp) cc_final: 0.7871 (mtp) REVERT: F 323 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.6789 (tpt90) REVERT: F 346 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7860 (mmtt) REVERT: F 437 MET cc_start: 0.7998 (tmm) cc_final: 0.7599 (tpp) REVERT: F 560 MET cc_start: 0.8073 (mtt) cc_final: 0.7848 (mtt) REVERT: G 138 LYS cc_start: 0.9156 (ptmm) cc_final: 0.8934 (pttm) REVERT: G 142 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8466 (pmm-80) REVERT: G 257 MET cc_start: 0.8445 (mmp) cc_final: 0.7569 (mmp) REVERT: G 378 SER cc_start: 0.7703 (m) cc_final: 0.7310 (t) REVERT: G 406 GLU cc_start: 0.8338 (tt0) cc_final: 0.8060 (tt0) outliers start: 50 outliers final: 11 residues processed: 529 average time/residue: 0.5236 time to fit residues: 427.9463 Evaluate side-chains 312 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 298 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 572 LEU Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 340 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 253 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN E 327 ASN E 337 GLN G 361 HIS K 240 GLN K 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.103460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.081947 restraints weight = 105623.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081267 restraints weight = 60298.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.082065 restraints weight = 54568.991| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35229 Z= 0.142 Angle : 0.618 9.040 47657 Z= 0.304 Chirality : 0.044 0.160 5364 Planarity : 0.004 0.055 6206 Dihedral : 9.899 175.031 5024 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 1.66 % Allowed : 7.09 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.56 (0.13), residues: 4330 helix: 2.04 (0.12), residues: 2096 sheet: -0.10 (0.21), residues: 622 loop : 0.27 (0.17), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 486 HIS 0.014 0.001 HIS C 719 PHE 0.014 0.001 PHE G 169 TYR 0.018 0.001 TYR G 439 ARG 0.007 0.000 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 1622) hydrogen bonds : angle 4.71314 ( 4602) metal coordination : bond 0.02093 ( 8) metal coordination : angle 2.29501 ( 6) covalent geometry : bond 0.00324 (35219) covalent geometry : angle 0.61710 (47651) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 327 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.7764 (m-70) cc_final: 0.7548 (m-70) REVERT: A 173 PHE cc_start: 0.7054 (m-80) cc_final: 0.6322 (m-80) REVERT: A 283 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 673 LYS cc_start: 0.8137 (ttpp) cc_final: 0.7848 (ptpp) REVERT: B 301 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7898 (tm-30) REVERT: B 522 LYS cc_start: 0.8307 (mttt) cc_final: 0.8095 (ttmt) REVERT: B 571 ASP cc_start: 0.8429 (t0) cc_final: 0.8051 (t0) REVERT: B 621 MET cc_start: 0.8494 (tpp) cc_final: 0.7728 (tpp) REVERT: C 215 ASP cc_start: 0.8732 (t0) cc_final: 0.8479 (t0) REVERT: C 326 THR cc_start: 0.6144 (t) cc_final: 0.5802 (m) REVERT: C 494 GLU cc_start: 0.7995 (pm20) cc_final: 0.7218 (pt0) REVERT: C 571 ASP cc_start: 0.8503 (t0) cc_final: 0.8244 (t0) REVERT: D 208 MET cc_start: 0.6138 (tpp) cc_final: 0.4751 (tpt) REVERT: D 304 GLU cc_start: 0.8083 (tp30) cc_final: 0.7795 (tp30) REVERT: D 493 ASP cc_start: 0.7925 (m-30) cc_final: 0.7591 (t70) REVERT: D 522 LYS cc_start: 0.8531 (tttt) cc_final: 0.8186 (tptm) REVERT: E 314 ASP cc_start: 0.8098 (t0) cc_final: 0.7731 (t70) REVERT: E 315 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8357 (mt-10) REVERT: E 346 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7516 (ptmt) REVERT: E 699 TYR cc_start: 0.8295 (t80) cc_final: 0.7880 (t80) REVERT: E 709 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.8001 (tt) REVERT: F 323 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.6971 (tpt90) REVERT: F 588 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: G 142 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8337 (ptt-90) REVERT: G 205 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.6094 (m-70) REVERT: G 233 MET cc_start: 0.8864 (mmm) cc_final: 0.8499 (mmm) REVERT: G 257 MET cc_start: 0.8271 (mmp) cc_final: 0.7847 (mmp) REVERT: G 378 SER cc_start: 0.7657 (m) cc_final: 0.7415 (t) REVERT: G 406 GLU cc_start: 0.8224 (tt0) cc_final: 0.7807 (tm-30) REVERT: G 440 MET cc_start: 0.8064 (ttm) cc_final: 0.7729 (mtp) REVERT: H 252 ARG cc_start: 0.6139 (mmt-90) cc_final: 0.5002 (mtm110) outliers start: 62 outliers final: 21 residues processed: 378 average time/residue: 0.4832 time to fit residues: 295.6020 Evaluate side-chains 300 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 139 optimal weight: 20.0000 chunk 408 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 385 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 197 optimal weight: 0.7980 chunk 374 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN C 161 HIS C 548 ASN E 295 ASN K 240 GLN L 325 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.101451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078713 restraints weight = 106148.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079812 restraints weight = 57684.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080097 restraints weight = 49254.580| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 35229 Z= 0.184 Angle : 0.609 7.922 47657 Z= 0.299 Chirality : 0.044 0.181 5364 Planarity : 0.004 0.059 6206 Dihedral : 9.405 162.594 5003 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.90 % Rotamer: Outliers : 1.53 % Allowed : 8.43 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 4330 helix: 1.84 (0.12), residues: 2096 sheet: -0.11 (0.20), residues: 613 loop : 0.10 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 486 HIS 0.014 0.001 HIS C 719 PHE 0.015 0.001 PHE D 275 TYR 0.017 0.001 TYR G 439 ARG 0.004 0.000 ARG E 348 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1622) hydrogen bonds : angle 4.64735 ( 4602) metal coordination : bond 0.03592 ( 8) metal coordination : angle 2.79093 ( 6) covalent geometry : bond 0.00428 (35219) covalent geometry : angle 0.60794 (47651) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 4.078 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 173 PHE cc_start: 0.6792 (m-80) cc_final: 0.6549 (m-80) REVERT: A 283 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 430 MET cc_start: 0.9043 (tpp) cc_final: 0.8436 (tpp) REVERT: B 571 ASP cc_start: 0.8476 (t0) cc_final: 0.8089 (t0) REVERT: B 621 MET cc_start: 0.8687 (tpp) cc_final: 0.8384 (tpp) REVERT: C 56 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5848 (tmm) REVERT: C 215 ASP cc_start: 0.8857 (t0) cc_final: 0.8614 (t0) REVERT: C 571 ASP cc_start: 0.8656 (t0) cc_final: 0.8313 (t0) REVERT: D 208 MET cc_start: 0.6312 (tpp) cc_final: 0.6057 (tpp) REVERT: D 493 ASP cc_start: 0.7972 (m-30) cc_final: 0.7585 (t70) REVERT: D 522 LYS cc_start: 0.8692 (tttt) cc_final: 0.8201 (tptm) REVERT: D 615 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9113 (mm) REVERT: E 332 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8207 (ttm-80) REVERT: E 346 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7566 (ptmt) REVERT: E 489 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8006 (p) REVERT: E 709 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7953 (tt) REVERT: F 253 MET cc_start: 0.8288 (mtp) cc_final: 0.8067 (mtp) REVERT: F 323 ARG cc_start: 0.8029 (tpp-160) cc_final: 0.7264 (tpt170) REVERT: F 430 MET cc_start: 0.8977 (tpp) cc_final: 0.8719 (tpp) REVERT: F 588 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: G 233 MET cc_start: 0.8818 (mmm) cc_final: 0.8499 (mmm) REVERT: G 257 MET cc_start: 0.8320 (mmp) cc_final: 0.7787 (mmp) REVERT: G 378 SER cc_start: 0.7832 (m) cc_final: 0.7443 (t) REVERT: G 406 GLU cc_start: 0.8425 (tt0) cc_final: 0.8112 (tm-30) REVERT: H 252 ARG cc_start: 0.6247 (mmt-90) cc_final: 0.4956 (mtm180) REVERT: J 140 GLN cc_start: 0.5226 (OUTLIER) cc_final: 0.4871 (pm20) REVERT: L 352 ASP cc_start: 0.6961 (m-30) cc_final: 0.6738 (t0) outliers start: 57 outliers final: 29 residues processed: 322 average time/residue: 0.4551 time to fit residues: 240.6614 Evaluate side-chains 293 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 140 GLN Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 19 optimal weight: 4.9990 chunk 380 optimal weight: 0.9980 chunk 272 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 421 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 309 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 GLN G 491 ASN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075109 restraints weight = 105494.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077113 restraints weight = 55591.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078371 restraints weight = 37740.926| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35229 Z= 0.170 Angle : 0.589 9.256 47657 Z= 0.287 Chirality : 0.043 0.216 5364 Planarity : 0.004 0.064 6206 Dihedral : 9.038 153.469 4997 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 1.75 % Allowed : 9.67 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.21 (0.13), residues: 4330 helix: 1.74 (0.12), residues: 2104 sheet: -0.12 (0.21), residues: 613 loop : 0.03 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 486 HIS 0.008 0.001 HIS C 719 PHE 0.014 0.001 PHE D 275 TYR 0.020 0.001 TYR G 439 ARG 0.006 0.000 ARG G 142 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 1622) hydrogen bonds : angle 4.53036 ( 4602) metal coordination : bond 0.03383 ( 8) metal coordination : angle 3.06998 ( 6) covalent geometry : bond 0.00393 (35219) covalent geometry : angle 0.58784 (47651) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 278 time to evaluate : 4.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7587 (tppt) REVERT: A 162 PHE cc_start: 0.2342 (p90) cc_final: 0.2122 (p90) REVERT: A 173 PHE cc_start: 0.7198 (m-80) cc_final: 0.6788 (m-80) REVERT: A 283 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 430 MET cc_start: 0.8999 (tpp) cc_final: 0.8490 (tpp) REVERT: A 673 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7862 (ptpp) REVERT: B 571 ASP cc_start: 0.8466 (t0) cc_final: 0.8026 (t0) REVERT: B 621 MET cc_start: 0.8795 (tpp) cc_final: 0.8272 (tpp) REVERT: B 762 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7606 (tmm) REVERT: C 215 ASP cc_start: 0.8912 (t0) cc_final: 0.8613 (t0) REVERT: C 571 ASP cc_start: 0.8670 (t0) cc_final: 0.8326 (t0) REVERT: D 493 ASP cc_start: 0.7951 (m-30) cc_final: 0.7562 (t70) REVERT: D 522 LYS cc_start: 0.8703 (tttt) cc_final: 0.8084 (tptm) REVERT: D 615 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9025 (mm) REVERT: E 332 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7767 (ttm-80) REVERT: E 346 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7247 (ptmm) REVERT: E 617 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: E 709 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7940 (tt) REVERT: F 253 MET cc_start: 0.8290 (mtp) cc_final: 0.8039 (mtp) REVERT: F 323 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7245 (tpt170) REVERT: F 430 MET cc_start: 0.8943 (tpp) cc_final: 0.8685 (tpp) REVERT: F 588 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: G 257 MET cc_start: 0.8286 (mmp) cc_final: 0.7780 (mmp) REVERT: G 378 SER cc_start: 0.8170 (m) cc_final: 0.7890 (t) REVERT: G 406 GLU cc_start: 0.8368 (tt0) cc_final: 0.8035 (tm-30) REVERT: H 252 ARG cc_start: 0.6391 (mmt-90) cc_final: 0.4928 (mtm180) outliers start: 65 outliers final: 40 residues processed: 328 average time/residue: 0.4457 time to fit residues: 244.5369 Evaluate side-chains 302 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 567 SER Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 140 optimal weight: 0.6980 chunk 262 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 347 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 426 optimal weight: 0.0370 overall best weight: 2.0462 ------------------------------------------------------------------------------- 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 B 651 GLN C 95 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.100756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.074829 restraints weight = 105599.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.076800 restraints weight = 55878.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.078044 restraints weight = 37985.406| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 35229 Z= 0.188 Angle : 0.606 11.578 47657 Z= 0.295 Chirality : 0.043 0.224 5364 Planarity : 0.004 0.065 6206 Dihedral : 8.799 145.838 4997 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.15 % Allowed : 10.42 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 4330 helix: 1.64 (0.12), residues: 2116 sheet: -0.13 (0.21), residues: 605 loop : -0.07 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 486 HIS 0.018 0.001 HIS C 719 PHE 0.016 0.001 PHE D 275 TYR 0.018 0.001 TYR G 439 ARG 0.012 0.000 ARG C 348 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1622) hydrogen bonds : angle 4.52370 ( 4602) metal coordination : bond 0.03674 ( 8) metal coordination : angle 3.55899 ( 6) covalent geometry : bond 0.00435 (35219) covalent geometry : angle 0.60445 (47651) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 263 time to evaluate : 4.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 TYR cc_start: 0.6957 (m-80) cc_final: 0.6751 (m-80) REVERT: A 158 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7674 (tppt) REVERT: A 173 PHE cc_start: 0.7280 (m-80) cc_final: 0.6848 (m-80) REVERT: A 283 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 430 MET cc_start: 0.9007 (tpp) cc_final: 0.8483 (tpp) REVERT: A 673 LYS cc_start: 0.8089 (ttpp) cc_final: 0.7818 (ptpp) REVERT: A 784 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6441 (mpp) REVERT: B 571 ASP cc_start: 0.8465 (t0) cc_final: 0.8015 (t0) REVERT: B 621 MET cc_start: 0.8919 (tpp) cc_final: 0.8420 (tpp) REVERT: B 762 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7624 (tmm) REVERT: C 215 ASP cc_start: 0.8936 (t0) cc_final: 0.8631 (t0) REVERT: C 342 MET cc_start: 0.9276 (mmm) cc_final: 0.9043 (mmt) REVERT: C 437 MET cc_start: 0.8431 (tpp) cc_final: 0.8149 (tpp) REVERT: C 571 ASP cc_start: 0.8717 (t0) cc_final: 0.8380 (t0) REVERT: C 784 MET cc_start: 0.8371 (tmm) cc_final: 0.8046 (mmt) REVERT: D 208 MET cc_start: 0.6155 (tpp) cc_final: 0.4943 (tpt) REVERT: D 493 ASP cc_start: 0.7979 (m-30) cc_final: 0.7574 (t70) REVERT: D 522 LYS cc_start: 0.8653 (tttt) cc_final: 0.8006 (tptm) REVERT: E 346 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7317 (ptmm) REVERT: E 489 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7985 (p) REVERT: E 514 THR cc_start: 0.8805 (m) cc_final: 0.8587 (p) REVERT: E 617 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: F 253 MET cc_start: 0.8357 (mtp) cc_final: 0.8083 (mtp) REVERT: F 323 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7202 (tpt170) REVERT: F 430 MET cc_start: 0.8960 (tpp) cc_final: 0.8685 (tpp) REVERT: G 257 MET cc_start: 0.8298 (mmp) cc_final: 0.7775 (mmp) REVERT: G 352 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8232 (p) REVERT: G 378 SER cc_start: 0.8238 (m) cc_final: 0.8005 (t) REVERT: G 406 GLU cc_start: 0.8344 (tt0) cc_final: 0.8075 (tt0) REVERT: H 252 ARG cc_start: 0.6573 (mmt-90) cc_final: 0.5046 (mtm110) outliers start: 80 outliers final: 51 residues processed: 326 average time/residue: 0.4518 time to fit residues: 248.5772 Evaluate side-chains 309 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 4.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 171 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 241 optimal weight: 6.9990 chunk 196 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 chunk 244 optimal weight: 0.1980 chunk 433 optimal weight: 3.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 95 ASN C 161 HIS F 432 GLN G 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.101806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075981 restraints weight = 104712.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.077979 restraints weight = 55069.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079260 restraints weight = 37245.788| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35229 Z= 0.119 Angle : 0.562 9.923 47657 Z= 0.272 Chirality : 0.042 0.219 5364 Planarity : 0.004 0.062 6206 Dihedral : 8.495 139.894 4997 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 1.72 % Allowed : 10.98 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.20 (0.13), residues: 4330 helix: 1.74 (0.12), residues: 2093 sheet: -0.10 (0.21), residues: 617 loop : 0.03 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 486 HIS 0.003 0.001 HIS C 757 PHE 0.013 0.001 PHE H 300 TYR 0.014 0.001 TYR G 439 ARG 0.004 0.000 ARG G 142 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 1622) hydrogen bonds : angle 4.32017 ( 4602) metal coordination : bond 0.02246 ( 8) metal coordination : angle 3.10408 ( 6) covalent geometry : bond 0.00270 (35219) covalent geometry : angle 0.56069 (47651) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 284 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7698 (tppt) REVERT: A 173 PHE cc_start: 0.7166 (m-80) cc_final: 0.6883 (m-80) REVERT: A 430 MET cc_start: 0.8956 (tpp) cc_final: 0.8438 (tpp) REVERT: A 536 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8527 (pp) REVERT: A 673 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7873 (ptpp) REVERT: A 784 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6379 (mpp) REVERT: B 301 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 571 ASP cc_start: 0.8397 (t0) cc_final: 0.7946 (t0) REVERT: B 621 MET cc_start: 0.8823 (tpp) cc_final: 0.8363 (tpp) REVERT: B 762 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7539 (tmm) REVERT: C 215 ASP cc_start: 0.8909 (t0) cc_final: 0.8625 (t0) REVERT: C 223 MET cc_start: 0.8907 (tpp) cc_final: 0.8676 (mmm) REVERT: C 342 MET cc_start: 0.9235 (mmm) cc_final: 0.9000 (mmt) REVERT: C 398 MET cc_start: 0.9111 (mmt) cc_final: 0.8841 (mmt) REVERT: C 437 MET cc_start: 0.8423 (tpp) cc_final: 0.8201 (tpp) REVERT: C 571 ASP cc_start: 0.8636 (t0) cc_final: 0.8314 (t0) REVERT: D 493 ASP cc_start: 0.7926 (m-30) cc_final: 0.7541 (t70) REVERT: D 522 LYS cc_start: 0.8652 (tttt) cc_final: 0.7961 (tptm) REVERT: D 621 MET cc_start: 0.7300 (tpt) cc_final: 0.6730 (tpt) REVERT: E 223 MET cc_start: 0.8931 (mmm) cc_final: 0.8619 (tpp) REVERT: E 346 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7210 (ptmm) REVERT: E 489 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7927 (p) REVERT: E 617 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: F 253 MET cc_start: 0.8292 (mtp) cc_final: 0.8013 (mtp) REVERT: F 323 ARG cc_start: 0.7944 (tpp-160) cc_final: 0.7136 (tpt170) REVERT: F 325 LYS cc_start: 0.6925 (tppt) cc_final: 0.6339 (mmpt) REVERT: F 430 MET cc_start: 0.8888 (tpp) cc_final: 0.8642 (tpp) REVERT: G 257 MET cc_start: 0.8234 (mmp) cc_final: 0.7766 (mmp) REVERT: G 352 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.8031 (p) REVERT: G 378 SER cc_start: 0.8101 (m) cc_final: 0.7686 (t) REVERT: G 406 GLU cc_start: 0.8270 (tt0) cc_final: 0.7997 (tt0) REVERT: G 440 MET cc_start: 0.7981 (mtp) cc_final: 0.7768 (mtp) REVERT: H 252 ARG cc_start: 0.6665 (mmt-90) cc_final: 0.5064 (mtm110) outliers start: 64 outliers final: 36 residues processed: 328 average time/residue: 0.4338 time to fit residues: 237.8409 Evaluate side-chains 300 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 256 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 356 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.101424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079426 restraints weight = 105548.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078807 restraints weight = 62664.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.079681 restraints weight = 51033.208| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35229 Z= 0.149 Angle : 0.591 11.111 47657 Z= 0.284 Chirality : 0.043 0.277 5364 Planarity : 0.004 0.120 6206 Dihedral : 8.346 137.652 4997 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 1.72 % Allowed : 11.52 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.18 (0.13), residues: 4330 helix: 1.72 (0.12), residues: 2099 sheet: -0.10 (0.21), residues: 615 loop : 0.01 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 486 HIS 0.003 0.001 HIS G 170 PHE 0.013 0.001 PHE G 509 TYR 0.014 0.001 TYR G 439 ARG 0.008 0.000 ARG G 203 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 1622) hydrogen bonds : angle 4.33810 ( 4602) metal coordination : bond 0.02830 ( 8) metal coordination : angle 3.90471 ( 6) covalent geometry : bond 0.00345 (35219) covalent geometry : angle 0.58960 (47651) Misc. bond : bond 0.00046 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7185 (tppt) REVERT: A 673 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7851 (ptpp) REVERT: A 784 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6342 (mpp) REVERT: B 301 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8001 (tm-30) REVERT: B 571 ASP cc_start: 0.8441 (t0) cc_final: 0.7960 (t0) REVERT: B 621 MET cc_start: 0.8884 (tpp) cc_final: 0.8406 (tpp) REVERT: B 762 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7523 (tmm) REVERT: C 215 ASP cc_start: 0.8826 (t0) cc_final: 0.8619 (t0) REVERT: C 223 MET cc_start: 0.8933 (tpp) cc_final: 0.8714 (mmm) REVERT: C 342 MET cc_start: 0.9247 (mmm) cc_final: 0.9014 (mmt) REVERT: C 437 MET cc_start: 0.8444 (tpp) cc_final: 0.8216 (tpp) REVERT: C 571 ASP cc_start: 0.8676 (t0) cc_final: 0.8336 (t0) REVERT: C 784 MET cc_start: 0.8342 (tmm) cc_final: 0.7988 (mmt) REVERT: D 208 MET cc_start: 0.6379 (tpp) cc_final: 0.4903 (tpt) REVERT: D 493 ASP cc_start: 0.8021 (m-30) cc_final: 0.7490 (t0) REVERT: D 522 LYS cc_start: 0.8614 (tttt) cc_final: 0.8040 (tptm) REVERT: D 621 MET cc_start: 0.7409 (tpt) cc_final: 0.6836 (tpt) REVERT: E 223 MET cc_start: 0.8922 (mmm) cc_final: 0.8628 (tpp) REVERT: E 346 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7432 (ptmm) REVERT: E 489 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8033 (p) REVERT: E 514 THR cc_start: 0.8879 (m) cc_final: 0.8635 (p) REVERT: E 617 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: F 246 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8610 (mmtp) REVERT: F 253 MET cc_start: 0.8350 (mtp) cc_final: 0.8070 (mtp) REVERT: F 323 ARG cc_start: 0.7994 (tpp-160) cc_final: 0.7079 (tpt170) REVERT: F 325 LYS cc_start: 0.7107 (tppt) cc_final: 0.6402 (mmpt) REVERT: F 430 MET cc_start: 0.8879 (tpp) cc_final: 0.8631 (tpp) REVERT: G 257 MET cc_start: 0.8287 (mmp) cc_final: 0.7782 (mmp) REVERT: G 352 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8070 (p) REVERT: G 378 SER cc_start: 0.7856 (m) cc_final: 0.7329 (t) REVERT: G 406 GLU cc_start: 0.8372 (tt0) cc_final: 0.8086 (tt0) REVERT: H 238 MET cc_start: 0.8598 (ttm) cc_final: 0.8302 (tpp) REVERT: H 252 ARG cc_start: 0.6702 (mmt-90) cc_final: 0.4978 (mtm110) outliers start: 64 outliers final: 50 residues processed: 306 average time/residue: 0.4196 time to fit residues: 215.3380 Evaluate side-chains 311 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 116 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 72 optimal weight: 0.0470 chunk 228 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 chunk 344 optimal weight: 2.9990 chunk 406 optimal weight: 2.9990 chunk 408 optimal weight: 8.9990 chunk 405 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.101265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078577 restraints weight = 105169.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.079704 restraints weight = 57018.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080012 restraints weight = 50185.162| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 35229 Z= 0.153 Angle : 0.597 11.740 47657 Z= 0.286 Chirality : 0.043 0.240 5364 Planarity : 0.004 0.062 6206 Dihedral : 8.266 139.021 4997 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.83 % Rotamer: Outliers : 1.88 % Allowed : 11.76 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.14 (0.13), residues: 4330 helix: 1.69 (0.12), residues: 2098 sheet: -0.11 (0.21), residues: 616 loop : -0.02 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 486 HIS 0.003 0.001 HIS G 468 PHE 0.012 0.001 PHE D 275 TYR 0.015 0.001 TYR G 439 ARG 0.003 0.000 ARG G 203 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 1622) hydrogen bonds : angle 4.35112 ( 4602) metal coordination : bond 0.03083 ( 8) metal coordination : angle 3.32506 ( 6) covalent geometry : bond 0.00354 (35219) covalent geometry : angle 0.59567 (47651) Misc. bond : bond 0.00056 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7082 (tppt) REVERT: A 412 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 673 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7882 (ptpp) REVERT: A 784 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6297 (mpp) REVERT: B 301 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 359 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.8147 (ttm110) REVERT: B 571 ASP cc_start: 0.8421 (t0) cc_final: 0.7936 (t0) REVERT: B 621 MET cc_start: 0.8900 (tpp) cc_final: 0.8421 (tpp) REVERT: B 762 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7618 (tmm) REVERT: C 398 MET cc_start: 0.9061 (mmt) cc_final: 0.8813 (mmt) REVERT: C 437 MET cc_start: 0.8463 (tpp) cc_final: 0.8235 (tpp) REVERT: C 494 GLU cc_start: 0.8211 (pm20) cc_final: 0.7205 (pt0) REVERT: C 571 ASP cc_start: 0.8701 (t0) cc_final: 0.8354 (t0) REVERT: D 208 MET cc_start: 0.6514 (tpp) cc_final: 0.5122 (tpt) REVERT: D 493 ASP cc_start: 0.8049 (m-30) cc_final: 0.7498 (t0) REVERT: D 522 LYS cc_start: 0.8614 (tttt) cc_final: 0.8003 (tptm) REVERT: D 621 MET cc_start: 0.7358 (tpt) cc_final: 0.7096 (tpt) REVERT: E 489 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8031 (p) REVERT: E 514 THR cc_start: 0.8873 (m) cc_final: 0.8617 (p) REVERT: E 617 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: F 253 MET cc_start: 0.8353 (mtp) cc_final: 0.8043 (mtp) REVERT: F 430 MET cc_start: 0.8888 (tpp) cc_final: 0.8640 (tpp) REVERT: G 257 MET cc_start: 0.8272 (mmp) cc_final: 0.7761 (mmp) REVERT: G 352 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8069 (p) REVERT: G 378 SER cc_start: 0.7905 (m) cc_final: 0.7372 (t) REVERT: G 406 GLU cc_start: 0.8332 (tt0) cc_final: 0.8062 (tt0) REVERT: H 238 MET cc_start: 0.8612 (ttm) cc_final: 0.8286 (tpp) REVERT: H 252 ARG cc_start: 0.6820 (mmt-90) cc_final: 0.4999 (mtm110) REVERT: L 348 LYS cc_start: 0.6669 (mmmt) cc_final: 0.6107 (ptpt) outliers start: 70 outliers final: 54 residues processed: 309 average time/residue: 0.4451 time to fit residues: 230.7869 Evaluate side-chains 313 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 347 optimal weight: 2.9990 chunk 410 optimal weight: 4.9990 chunk 425 optimal weight: 2.9990 chunk 417 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 265 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 719 HIS K 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.078558 restraints weight = 104934.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.079703 restraints weight = 55863.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080005 restraints weight = 48915.426| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35229 Z= 0.131 Angle : 0.594 12.140 47657 Z= 0.284 Chirality : 0.042 0.285 5364 Planarity : 0.004 0.062 6206 Dihedral : 8.169 137.238 4993 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.17 % Favored : 94.80 % Rotamer: Outliers : 1.83 % Allowed : 12.00 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 4330 helix: 1.71 (0.12), residues: 2092 sheet: -0.07 (0.21), residues: 616 loop : -0.01 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 486 HIS 0.022 0.001 HIS C 719 PHE 0.012 0.001 PHE H 300 TYR 0.012 0.001 TYR G 439 ARG 0.005 0.000 ARG C 348 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 1622) hydrogen bonds : angle 4.29873 ( 4602) metal coordination : bond 0.02407 ( 8) metal coordination : angle 3.49595 ( 6) covalent geometry : bond 0.00300 (35219) covalent geometry : angle 0.59292 (47651) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 4.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7856 (mmtt) cc_final: 0.6952 (tppt) REVERT: A 223 MET cc_start: 0.8893 (mmm) cc_final: 0.8392 (mmm) REVERT: A 673 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7918 (ptpp) REVERT: A 784 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6284 (mpp) REVERT: B 301 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 359 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8116 (ttm110) REVERT: B 571 ASP cc_start: 0.8405 (t0) cc_final: 0.7927 (t0) REVERT: B 621 MET cc_start: 0.8863 (tpp) cc_final: 0.8377 (tpp) REVERT: B 762 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7555 (tmm) REVERT: C 398 MET cc_start: 0.9092 (mmt) cc_final: 0.8852 (mmt) REVERT: C 437 MET cc_start: 0.8444 (tpp) cc_final: 0.8219 (tpp) REVERT: C 494 GLU cc_start: 0.8117 (pm20) cc_final: 0.7150 (pt0) REVERT: C 571 ASP cc_start: 0.8681 (t0) cc_final: 0.8341 (t0) REVERT: C 784 MET cc_start: 0.8390 (tmm) cc_final: 0.7991 (mmt) REVERT: D 208 MET cc_start: 0.6544 (tpp) cc_final: 0.5246 (tpt) REVERT: D 493 ASP cc_start: 0.8019 (m-30) cc_final: 0.7562 (t70) REVERT: D 522 LYS cc_start: 0.8620 (tttt) cc_final: 0.7989 (tptm) REVERT: E 223 MET cc_start: 0.8780 (mmm) cc_final: 0.7958 (mtm) REVERT: E 489 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7966 (p) REVERT: E 514 THR cc_start: 0.8873 (m) cc_final: 0.8617 (p) REVERT: F 253 MET cc_start: 0.8336 (mtp) cc_final: 0.8027 (mtp) REVERT: F 430 MET cc_start: 0.8879 (tpp) cc_final: 0.8633 (tpp) REVERT: G 257 MET cc_start: 0.8276 (mmp) cc_final: 0.7747 (mmp) REVERT: G 352 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8018 (p) REVERT: G 378 SER cc_start: 0.7859 (m) cc_final: 0.7312 (t) REVERT: G 406 GLU cc_start: 0.8241 (tt0) cc_final: 0.7960 (tt0) REVERT: H 238 MET cc_start: 0.8591 (ttm) cc_final: 0.8293 (tpp) REVERT: H 252 ARG cc_start: 0.6924 (mmt-90) cc_final: 0.5030 (mtm110) REVERT: L 348 LYS cc_start: 0.6689 (mmmt) cc_final: 0.6105 (ptpt) outliers start: 68 outliers final: 53 residues processed: 308 average time/residue: 0.4761 time to fit residues: 247.8837 Evaluate side-chains 309 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 325 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 285 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 419 optimal weight: 5.9990 chunk 417 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS F 432 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN L 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.099950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.077243 restraints weight = 105353.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078524 restraints weight = 57388.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078714 restraints weight = 50479.638| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 35229 Z= 0.210 Angle : 0.648 12.199 47657 Z= 0.314 Chirality : 0.044 0.285 5364 Planarity : 0.004 0.062 6206 Dihedral : 8.204 137.252 4990 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 1.66 % Allowed : 12.08 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.03 (0.13), residues: 4330 helix: 1.60 (0.12), residues: 2106 sheet: -0.16 (0.21), residues: 606 loop : -0.09 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 486 HIS 0.039 0.001 HIS C 719 PHE 0.016 0.002 PHE D 275 TYR 0.015 0.001 TYR D 254 ARG 0.007 0.000 ARG C 717 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1622) hydrogen bonds : angle 4.47967 ( 4602) metal coordination : bond 0.03823 ( 8) metal coordination : angle 4.20487 ( 6) covalent geometry : bond 0.00485 (35219) covalent geometry : angle 0.64681 (47651) Misc. bond : bond 0.00083 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7756 (mmtt) cc_final: 0.6786 (tppt) REVERT: A 223 MET cc_start: 0.8902 (mmm) cc_final: 0.8379 (mmm) REVERT: A 673 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7891 (ptpp) REVERT: A 784 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6348 (mpp) REVERT: B 359 ARG cc_start: 0.8487 (tpp-160) cc_final: 0.8161 (ttm110) REVERT: B 571 ASP cc_start: 0.8445 (t0) cc_final: 0.7963 (t0) REVERT: B 621 MET cc_start: 0.8968 (tpp) cc_final: 0.8507 (tpp) REVERT: B 762 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7594 (tmm) REVERT: C 398 MET cc_start: 0.9079 (mmt) cc_final: 0.8798 (mmt) REVERT: C 437 MET cc_start: 0.8548 (tpp) cc_final: 0.8247 (tpp) REVERT: C 494 GLU cc_start: 0.8153 (pm20) cc_final: 0.7169 (pt0) REVERT: C 571 ASP cc_start: 0.8757 (t0) cc_final: 0.8385 (t0) REVERT: C 784 MET cc_start: 0.8380 (tmm) cc_final: 0.7954 (mmt) REVERT: D 208 MET cc_start: 0.6525 (tpp) cc_final: 0.5278 (tpt) REVERT: D 493 ASP cc_start: 0.8028 (m-30) cc_final: 0.7528 (t0) REVERT: D 522 LYS cc_start: 0.8647 (tttt) cc_final: 0.7988 (tptm) REVERT: E 223 MET cc_start: 0.8665 (mmm) cc_final: 0.8040 (mtm) REVERT: E 229 MET cc_start: 0.8523 (tpp) cc_final: 0.8306 (tpp) REVERT: E 489 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8037 (p) REVERT: E 514 THR cc_start: 0.8957 (m) cc_final: 0.8690 (p) REVERT: F 253 MET cc_start: 0.8382 (mtp) cc_final: 0.8089 (mtp) REVERT: F 430 MET cc_start: 0.8915 (tpp) cc_final: 0.8654 (tpp) REVERT: G 257 MET cc_start: 0.8338 (mmp) cc_final: 0.7845 (mmp) REVERT: G 352 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8208 (p) REVERT: G 378 SER cc_start: 0.8048 (m) cc_final: 0.7548 (t) REVERT: G 406 GLU cc_start: 0.8235 (tt0) cc_final: 0.7967 (tt0) REVERT: H 238 MET cc_start: 0.8587 (ttm) cc_final: 0.8295 (tpp) REVERT: H 252 ARG cc_start: 0.7049 (mmt-90) cc_final: 0.5127 (mtm110) REVERT: L 348 LYS cc_start: 0.6972 (mmmt) cc_final: 0.5948 (ptpp) outliers start: 62 outliers final: 57 residues processed: 296 average time/residue: 0.4240 time to fit residues: 212.8751 Evaluate side-chains 312 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 325 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 377 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 401 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 296 optimal weight: 0.0050 chunk 68 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS F 432 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080907 restraints weight = 104926.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080079 restraints weight = 59193.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081084 restraints weight = 56176.847| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35229 Z= 0.114 Angle : 0.600 12.582 47657 Z= 0.287 Chirality : 0.042 0.245 5364 Planarity : 0.004 0.062 6206 Dihedral : 8.098 136.372 4990 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.15 % Rotamer: Outliers : 1.53 % Allowed : 12.35 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.13), residues: 4330 helix: 1.68 (0.12), residues: 2087 sheet: -0.11 (0.21), residues: 613 loop : -0.01 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 486 HIS 0.030 0.001 HIS C 719 PHE 0.013 0.001 PHE H 300 TYR 0.012 0.001 TYR G 439 ARG 0.006 0.000 ARG C 717 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 1622) hydrogen bonds : angle 4.29319 ( 4602) metal coordination : bond 0.01840 ( 8) metal coordination : angle 3.76153 ( 6) covalent geometry : bond 0.00257 (35219) covalent geometry : angle 0.59888 (47651) Misc. bond : bond 0.00027 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11135.80 seconds wall clock time: 193 minutes 59.58 seconds (11639.58 seconds total)