Starting phenix.real_space_refine on Sat Mar 7 05:06:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qx8_4663/03_2026/6qx8_4663.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qx8_4663/03_2026/6qx8_4663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qx8_4663/03_2026/6qx8_4663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qx8_4663/03_2026/6qx8_4663.map" model { file = "/net/cci-nas-00/data/ceres_data/6qx8_4663/03_2026/6qx8_4663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qx8_4663/03_2026/6qx8_4663.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.005 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 P 24 5.49 5 S 134 5.16 5 C 12272 2.51 5 N 3372 2.21 5 O 3742 1.98 5 H 19050 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38594 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 8141 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 486} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 9631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 9631 Classifications: {'peptide': 611} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 582} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1129 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 396 Classifications: {'RNA': 12} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "E" Number of atoms: 8141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 8141 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 486} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 9631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 9631 Classifications: {'peptide': 611} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 582} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1129 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 396 Classifications: {'RNA': 12} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Time building chain proxies: 6.45, per 1000 atoms: 0.17 Number of scatterers: 38594 At special positions: 0 Unit cell: (192.955, 103.257, 91.784, 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) S 134 16.00 P 24 15.00 O 3742 8.00 N 3372 7.00 C 12272 6.00 H 19050 1.00 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=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4492 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 16 sheets defined 48.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 4.106A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.841A pdb=" N ASP A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.746A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.048A pdb=" N CYS A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.596A pdb=" N TYR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 476 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 581 through 603 Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.251A pdb=" N GLU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.503A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 16 through 22 removed outlier: 4.513A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.690A pdb=" N VAL B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.677A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 161' Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 245 through 266 removed outlier: 3.678A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.589A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.741A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.816A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 5.417A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.833A pdb=" N SER B 422 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 521 through 536 Processing helix chain 'B' and resid 540 through 560 removed outlier: 4.077A pdb=" N MET B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.793A pdb=" N LEU B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.998A pdb=" N LEU B 611 " --> pdb=" O PRO B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.168A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.832A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.740A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 240 through 249 removed outlier: 4.106A pdb=" N GLY E 244 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.841A pdb=" N ASP E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE E 314 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 351 removed outlier: 3.746A pdb=" N TYR E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 380 through 386 removed outlier: 4.048A pdb=" N CYS E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 416 Processing helix chain 'E' and resid 433 through 452 removed outlier: 3.596A pdb=" N TYR E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 476 Processing helix chain 'E' and resid 572 through 580 Processing helix chain 'E' and resid 581 through 603 Processing helix chain 'E' and resid 608 through 613 removed outlier: 4.252A pdb=" N GLU E 613 " --> pdb=" O LYS E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 650 Processing helix chain 'E' and resid 652 through 674 removed outlier: 3.503A pdb=" N GLU E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 694 Processing helix chain 'E' and resid 697 through 715 Processing helix chain 'F' and resid 7 through 12 Processing helix chain 'F' and resid 16 through 22 removed outlier: 4.513A pdb=" N SER F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 50 Processing helix chain 'F' and resid 84 through 99 removed outlier: 3.690A pdb=" N VAL F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 117 Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 138 through 153 Processing helix chain 'F' and resid 156 through 161 removed outlier: 3.678A pdb=" N SER F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 156 through 161' Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'F' and resid 213 through 222 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.677A pdb=" N GLY F 250 " --> pdb=" O MET F 246 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE F 251 " --> pdb=" O GLN F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 291 removed outlier: 3.590A pdb=" N ALA F 283 " --> pdb=" O LYS F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 removed outlier: 3.741A pdb=" N GLN F 313 " --> pdb=" O TRP F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.816A pdb=" N PHE F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 345 removed outlier: 5.417A pdb=" N ALA F 340 " --> pdb=" O VAL F 336 " (cutoff:3.500A) Proline residue: F 341 - end of helix Processing helix chain 'F' and resid 371 through 373 No H-bonds generated for 'chain 'F' and resid 371 through 373' Processing helix chain 'F' and resid 382 through 393 Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.834A pdb=" N SER F 422 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 423 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 427 " --> pdb=" O ILE F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 473 Processing helix chain 'F' and resid 521 through 536 Processing helix chain 'F' and resid 540 through 560 removed outlier: 4.077A pdb=" N MET F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 583 removed outlier: 3.793A pdb=" N LEU F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 581 " --> pdb=" O LYS F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.997A pdb=" N LEU F 611 " --> pdb=" O PRO F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 616 No H-bonds generated for 'chain 'F' and resid 614 through 616' Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.168A pdb=" N MET G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 100 removed outlier: 3.832A pdb=" N VAL G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.740A pdb=" N TYR G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE G 119 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 125 " --> pdb=" O LYS G 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 490 removed outlier: 5.900A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 501 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 525 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 524 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 564 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 559 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.932A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 621 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.510A pdb=" N ASP B 130 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.716A pdb=" N ILE B 397 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 400 " --> pdb=" O ILE B 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 437 through 441 removed outlier: 3.620A pdb=" N TRP B 437 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 441 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.497A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 59 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 390 through 391 Processing sheet with id=AB1, first strand: chain 'E' and resid 481 through 490 removed outlier: 5.898A pdb=" N GLN E 481 " --> pdb=" O ILE E 505 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE E 505 " --> pdb=" O GLN E 481 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE E 483 " --> pdb=" O PHE E 503 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE E 503 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET E 485 " --> pdb=" O TYR E 501 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 501 " --> pdb=" O MET E 485 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR E 501 " --> pdb=" O PHE E 525 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E 525 " --> pdb=" O TYR E 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU E 524 " --> pdb=" O TYR E 564 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E 564 " --> pdb=" O GLU E 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG E 559 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU E 563 " --> pdb=" O GLU E 544 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLU E 544 " --> pdb=" O LEU E 563 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E 565 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL E 542 " --> pdb=" O VAL E 565 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 627 through 631 removed outlier: 6.933A pdb=" N GLY E 627 " --> pdb=" O GLU E 623 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU E 623 " --> pdb=" O GLY E 627 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU E 629 " --> pdb=" O ILE E 621 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 621 " --> pdb=" O GLU E 629 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 55 through 57 Processing sheet with id=AB4, first strand: chain 'F' and resid 128 through 130 removed outlier: 3.510A pdb=" N ASP F 130 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 135 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 396 through 397 removed outlier: 3.717A pdb=" N ILE F 397 " --> pdb=" O THR F 400 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 400 " --> pdb=" O ILE F 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 437 through 441 removed outlier: 3.619A pdb=" N TRP F 437 " --> pdb=" O ASN F 452 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 441 " --> pdb=" O ALA F 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 667 through 668 removed outlier: 4.347A pdb=" N ILE F 667 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 57 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 59 " --> pdb=" O VAL G 89 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2388 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: 9.94 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.47 - 0.74: 2 0.74 - 1.01: 19010 1.01 - 1.28: 3228 1.28 - 1.55: 16521 1.55 - 1.82: 305 Warning: very small bond lengths. Bond restraints: 39066 Sorted by residual: bond pdb=" N2 G H 12 " pdb=" H21 G H 12 " ideal model delta sigma weight residual 0.860 0.467 0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" N2 G D 12 " pdb=" H21 G D 12 " ideal model delta sigma weight residual 0.860 0.472 0.388 2.00e-02 2.50e+03 3.76e+02 bond pdb=" ND2 ASN F 532 " pdb="HD22 ASN F 532 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN F 532 " pdb="HD21 ASN F 532 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" NZ LYS F 531 " pdb=" HZ2 LYS F 531 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 39061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 23.64: 70552 23.64 - 47.29: 1 47.29 - 70.93: 3 70.93 - 94.57: 0 94.57 - 118.21: 2 Bond angle restraints: 70558 Sorted by residual: angle pdb=" C2 G H 12 " pdb=" N2 G H 12 " pdb=" H21 G H 12 " ideal model delta sigma weight residual 120.00 1.79 118.21 3.00e+00 1.11e-01 1.55e+03 angle pdb=" C2 G D 12 " pdb=" N2 G D 12 " pdb=" H21 G D 12 " ideal model delta sigma weight residual 120.00 4.49 115.51 3.00e+00 1.11e-01 1.48e+03 angle pdb=" CA GLY F 35 " pdb=" N GLY F 35 " pdb=" H GLY F 35 " ideal model delta sigma weight residual 114.26 58.70 55.57 3.00e+00 1.11e-01 3.43e+02 angle pdb=" C THR F 34 " pdb=" N GLY F 35 " pdb=" H GLY F 35 " ideal model delta sigma weight residual 124.56 69.21 55.35 3.00e+00 1.11e-01 3.40e+02 angle pdb=" C THR B 34 " pdb=" N GLY B 35 " pdb=" H GLY B 35 " ideal model delta sigma weight residual 124.55 74.32 50.24 3.00e+00 1.11e-01 2.80e+02 ... (remaining 70553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 15815 17.66 - 35.33: 1973 35.33 - 52.99: 458 52.99 - 70.66: 135 70.66 - 88.32: 33 Dihedral angle restraints: 18414 sinusoidal: 10292 harmonic: 8122 Sorted by residual: dihedral pdb=" CA SER A 571 " pdb=" C SER A 571 " pdb=" N LYS A 572 " pdb=" CA LYS A 572 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA SER E 571 " pdb=" C SER E 571 " pdb=" N LYS E 572 " pdb=" CA LYS E 572 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LEU E 283 " pdb=" C LEU E 283 " pdb=" N LEU E 284 " pdb=" CA LEU E 284 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 18411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2580 0.067 - 0.134: 374 0.134 - 0.201: 33 0.201 - 0.267: 3 0.267 - 0.334: 2 Chirality restraints: 2992 Sorted by residual: chirality pdb=" CA SER B 511 " pdb=" N SER B 511 " pdb=" C SER B 511 " pdb=" CB SER B 511 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA SER F 511 " pdb=" N SER F 511 " pdb=" C SER F 511 " pdb=" CB SER F 511 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA THR F 528 " pdb=" N THR F 528 " pdb=" C THR F 528 " pdb=" CB THR F 528 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2989 not shown) Planarity restraints: 5686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 514 " -0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" N SER B 515 " 0.067 2.00e-02 2.50e+03 pdb=" CA SER B 515 " -0.017 2.00e-02 2.50e+03 pdb=" H SER B 515 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 530 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C PRO E 530 " 0.066 2.00e-02 2.50e+03 pdb=" O PRO E 530 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG E 531 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 530 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C PRO A 530 " -0.066 2.00e-02 2.50e+03 pdb=" O PRO A 530 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG A 531 " 0.022 2.00e-02 2.50e+03 ... (remaining 5683 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.93: 239 1.93 - 2.60: 46957 2.60 - 3.27: 119734 3.27 - 3.93: 146384 3.93 - 4.60: 233822 Nonbonded interactions: 547136 Sorted by model distance: nonbonded pdb=" HE1 TYR F 24 " pdb=" HG3 PRO F 28 " model vdw 1.268 2.270 nonbonded pdb="HH11 ARG E 583 " pdb=" H SER F 511 " model vdw 1.508 2.100 nonbonded pdb=" H ILE F 517 " pdb=" OD2 ASP F 522 " model vdw 1.515 2.450 nonbonded pdb=" H ILE B 517 " pdb=" OD2 ASP B 522 " model vdw 1.526 2.450 nonbonded pdb="HH11 ARG A 583 " pdb=" H SER B 511 " model vdw 1.538 2.100 ... (remaining 547131 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.470 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: 0.190 Extract box with map and model: 0.330 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.740 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 : 0.008 0.082 20016 Z= 0.365 Angle : 0.938 19.692 27182 Z= 0.519 Chirality : 0.047 0.334 2992 Planarity : 0.007 0.085 3412 Dihedral : 15.538 88.323 7686 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.97 % Favored : 91.86 % Rotamer: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.15), residues: 2360 helix: -1.90 (0.13), residues: 1046 sheet: -3.80 (0.32), residues: 184 loop : -2.82 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 716 TYR 0.018 0.002 TYR B 467 PHE 0.030 0.002 PHE E 520 TRP 0.014 0.003 TRP E 577 HIS 0.008 0.002 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00816 (20016) covalent geometry : angle 0.93845 (27182) hydrogen bonds : bond 0.17331 ( 817) hydrogen bonds : angle 7.40950 ( 2388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 503 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 500 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7745 (pm20) cc_final: 0.7458 (mp0) REVERT: A 460 MET cc_start: 0.7212 (mmt) cc_final: 0.6785 (mtt) REVERT: A 480 PHE cc_start: 0.7655 (m-10) cc_final: 0.7445 (m-10) REVERT: A 496 ARG cc_start: 0.5920 (ptp90) cc_final: 0.5400 (ptt180) REVERT: A 650 TYR cc_start: 0.8848 (m-80) cc_final: 0.8630 (m-10) REVERT: B 70 ASP cc_start: 0.6171 (m-30) cc_final: 0.5011 (t0) REVERT: B 87 CYS cc_start: 0.8402 (m) cc_final: 0.7991 (m) REVERT: B 105 ASN cc_start: 0.9027 (m-40) cc_final: 0.8820 (m-40) REVERT: B 111 MET cc_start: 0.7048 (mmm) cc_final: 0.6841 (mmm) REVERT: B 127 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6994 (mm-40) REVERT: B 343 MET cc_start: 0.7827 (ptp) cc_final: 0.7569 (ptp) REVERT: B 348 MET cc_start: 0.6876 (ttm) cc_final: 0.5692 (pmm) REVERT: B 439 ASP cc_start: 0.7762 (t0) cc_final: 0.7552 (t0) REVERT: B 470 CYS cc_start: 0.8445 (t) cc_final: 0.8203 (t) REVERT: C 78 TRP cc_start: 0.7298 (p-90) cc_final: 0.6096 (p-90) REVERT: E 370 LEU cc_start: 0.8410 (mt) cc_final: 0.8141 (mt) REVERT: E 460 MET cc_start: 0.7201 (mmt) cc_final: 0.6857 (mtt) REVERT: E 496 ARG cc_start: 0.5868 (ptp90) cc_final: 0.5319 (ptt180) REVERT: E 661 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7184 (mm-30) REVERT: E 706 TRP cc_start: 0.7097 (m-10) cc_final: 0.6160 (m-10) REVERT: F 70 ASP cc_start: 0.6089 (m-30) cc_final: 0.4933 (t0) REVERT: F 87 CYS cc_start: 0.8463 (m) cc_final: 0.8229 (m) REVERT: F 105 ASN cc_start: 0.9053 (m-40) cc_final: 0.8792 (m-40) REVERT: F 127 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6756 (mm-40) REVERT: F 348 MET cc_start: 0.6559 (ttm) cc_final: 0.5618 (pmm) REVERT: F 439 ASP cc_start: 0.7839 (t0) cc_final: 0.7608 (t0) REVERT: F 470 CYS cc_start: 0.8246 (t) cc_final: 0.8024 (t) REVERT: F 554 ASP cc_start: 0.8567 (t0) cc_final: 0.8355 (t0) REVERT: G 71 ASN cc_start: 0.7926 (p0) cc_final: 0.7624 (p0) REVERT: G 78 TRP cc_start: 0.7302 (p-90) cc_final: 0.6042 (p-90) outliers start: 3 outliers final: 0 residues processed: 502 average time/residue: 0.3473 time to fit residues: 254.5238 Evaluate side-chains 395 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN B 312 ASN B 621 GLN E 383 ASN ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 GLN F 621 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.169516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143778 restraints weight = 103432.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148940 restraints weight = 53441.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152376 restraints weight = 33730.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.154584 restraints weight = 24401.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.155953 restraints weight = 19524.552| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20016 Z= 0.161 Angle : 0.672 24.445 27182 Z= 0.360 Chirality : 0.039 0.172 2992 Planarity : 0.006 0.079 3412 Dihedral : 10.445 84.053 2936 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.86 % Favored : 93.01 % Rotamer: Outliers : 0.05 % Allowed : 3.35 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.16), residues: 2360 helix: -0.83 (0.14), residues: 1082 sheet: -3.49 (0.34), residues: 192 loop : -2.62 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 101 TYR 0.017 0.002 TYR F 467 PHE 0.020 0.002 PHE B 466 TRP 0.010 0.001 TRP E 619 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00349 (20016) covalent geometry : angle 0.67245 (27182) hydrogen bonds : bond 0.05805 ( 817) hydrogen bonds : angle 6.02945 ( 2388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 465 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 464 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8167 (mp) cc_final: 0.7477 (tp) REVERT: A 460 MET cc_start: 0.7193 (mmt) cc_final: 0.6542 (mtt) REVERT: A 496 ARG cc_start: 0.6066 (ptp90) cc_final: 0.5225 (ptt180) REVERT: A 575 MET cc_start: 0.7315 (mtp) cc_final: 0.6978 (mtp) REVERT: B 87 CYS cc_start: 0.8468 (m) cc_final: 0.8006 (m) REVERT: B 105 ASN cc_start: 0.8834 (m-40) cc_final: 0.8375 (t0) REVERT: B 111 MET cc_start: 0.6767 (mmm) cc_final: 0.6530 (mmm) REVERT: B 343 MET cc_start: 0.7808 (ptp) cc_final: 0.7500 (ptp) REVERT: B 386 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7551 (ttm170) REVERT: B 439 ASP cc_start: 0.7836 (t0) cc_final: 0.7509 (t0) REVERT: B 508 GLU cc_start: 0.8258 (pm20) cc_final: 0.7990 (pm20) REVERT: B 514 VAL cc_start: 0.8481 (m) cc_final: 0.8015 (p) REVERT: C 60 ASP cc_start: 0.8214 (p0) cc_final: 0.7991 (p0) REVERT: E 438 ILE cc_start: 0.8299 (mp) cc_final: 0.7539 (tp) REVERT: E 460 MET cc_start: 0.7226 (mmt) cc_final: 0.6676 (mtt) REVERT: E 496 ARG cc_start: 0.5660 (ptp90) cc_final: 0.5157 (ptt180) REVERT: E 535 HIS cc_start: 0.5524 (p-80) cc_final: 0.5164 (p-80) REVERT: F 87 CYS cc_start: 0.8556 (m) cc_final: 0.8283 (m) REVERT: F 105 ASN cc_start: 0.8867 (m-40) cc_final: 0.8310 (t0) REVERT: F 124 GLN cc_start: 0.7460 (mp10) cc_final: 0.6805 (pp30) REVERT: F 439 ASP cc_start: 0.7690 (t0) cc_final: 0.7415 (t0) REVERT: F 545 GLN cc_start: 0.8189 (mt0) cc_final: 0.7841 (mt0) REVERT: F 554 ASP cc_start: 0.8564 (t0) cc_final: 0.8361 (t0) REVERT: G 78 TRP cc_start: 0.7533 (p-90) cc_final: 0.6194 (p-90) REVERT: G 81 MET cc_start: 0.6199 (mpp) cc_final: 0.5979 (ptt) outliers start: 1 outliers final: 1 residues processed: 465 average time/residue: 0.3090 time to fit residues: 219.2649 Evaluate side-chains 391 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 111 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 225 optimal weight: 0.9990 chunk 172 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 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 = 0.4124 r_free = 0.4124 target = 0.170290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144558 restraints weight = 102538.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149961 restraints weight = 51279.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153418 restraints weight = 31421.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155660 restraints weight = 22435.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157076 restraints weight = 17796.868| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20016 Z= 0.137 Angle : 0.626 24.201 27182 Z= 0.330 Chirality : 0.038 0.178 2992 Planarity : 0.005 0.062 3412 Dihedral : 10.208 80.897 2936 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.17), residues: 2360 helix: -0.30 (0.15), residues: 1074 sheet: -3.22 (0.34), residues: 192 loop : -2.29 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 443 TYR 0.011 0.001 TYR F 431 PHE 0.020 0.001 PHE E 480 TRP 0.010 0.001 TRP A 619 HIS 0.002 0.000 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00300 (20016) covalent geometry : angle 0.62557 (27182) hydrogen bonds : bond 0.05315 ( 817) hydrogen bonds : angle 5.62226 ( 2388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 438 ILE cc_start: 0.8099 (mp) cc_final: 0.7394 (tp) REVERT: A 460 MET cc_start: 0.7283 (mmt) cc_final: 0.6710 (mtt) REVERT: A 496 ARG cc_start: 0.5927 (ptp90) cc_final: 0.5233 (ptt180) REVERT: B 105 ASN cc_start: 0.8778 (m-40) cc_final: 0.8357 (t0) REVERT: B 111 MET cc_start: 0.6688 (mmm) cc_final: 0.6448 (mmm) REVERT: B 226 THR cc_start: 0.5285 (p) cc_final: 0.4956 (p) REVERT: B 343 MET cc_start: 0.7848 (ptp) cc_final: 0.7534 (ptp) REVERT: B 372 MET cc_start: 0.8013 (ppp) cc_final: 0.7546 (tmm) REVERT: B 386 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7315 (tmm160) REVERT: B 439 ASP cc_start: 0.7811 (t0) cc_final: 0.7484 (t0) REVERT: B 508 GLU cc_start: 0.8236 (pm20) cc_final: 0.8003 (pm20) REVERT: B 545 GLN cc_start: 0.8111 (mt0) cc_final: 0.7664 (mt0) REVERT: C 60 ASP cc_start: 0.8241 (p0) cc_final: 0.8024 (p0) REVERT: E 438 ILE cc_start: 0.8243 (mp) cc_final: 0.7707 (tp) REVERT: E 460 MET cc_start: 0.7244 (mmt) cc_final: 0.6631 (mtt) REVERT: E 496 ARG cc_start: 0.5541 (ptp90) cc_final: 0.5260 (ptt180) REVERT: E 535 HIS cc_start: 0.5467 (p-80) cc_final: 0.5022 (p-80) REVERT: F 87 CYS cc_start: 0.8367 (m) cc_final: 0.8104 (m) REVERT: F 105 ASN cc_start: 0.8780 (m-40) cc_final: 0.8306 (t0) REVERT: F 372 MET cc_start: 0.7847 (ppp) cc_final: 0.7606 (tmm) REVERT: F 386 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7143 (tmm160) REVERT: F 439 ASP cc_start: 0.7829 (t0) cc_final: 0.7468 (t0) REVERT: F 455 ASN cc_start: 0.8058 (p0) cc_final: 0.7858 (p0) REVERT: F 545 GLN cc_start: 0.7747 (mt0) cc_final: 0.7536 (mt0) REVERT: F 560 ARG cc_start: 0.8082 (mpt180) cc_final: 0.7864 (mmt90) REVERT: G 78 TRP cc_start: 0.7496 (p-90) cc_final: 0.6187 (p-90) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.3211 time to fit residues: 227.6808 Evaluate side-chains 398 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.167744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141268 restraints weight = 103697.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.146543 restraints weight = 51997.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149976 restraints weight = 32226.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152226 restraints weight = 23223.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153702 restraints weight = 18520.052| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20016 Z= 0.181 Angle : 0.628 24.436 27182 Z= 0.333 Chirality : 0.038 0.163 2992 Planarity : 0.005 0.059 3412 Dihedral : 10.154 79.584 2936 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.17), residues: 2360 helix: -0.07 (0.15), residues: 1076 sheet: -3.17 (0.35), residues: 192 loop : -2.28 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 443 TYR 0.012 0.001 TYR B 467 PHE 0.015 0.001 PHE B 466 TRP 0.009 0.001 TRP E 406 HIS 0.004 0.001 HIS F 664 Details of bonding type rmsd covalent geometry : bond 0.00388 (20016) covalent geometry : angle 0.62771 (27182) hydrogen bonds : bond 0.05101 ( 817) hydrogen bonds : angle 5.52832 ( 2388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8172 (mp) cc_final: 0.7526 (tp) REVERT: A 460 MET cc_start: 0.7263 (mmt) cc_final: 0.6674 (mtt) REVERT: A 496 ARG cc_start: 0.5994 (ptp90) cc_final: 0.5322 (ptt180) REVERT: A 523 MET cc_start: 0.8669 (mtt) cc_final: 0.8445 (mtt) REVERT: A 575 MET cc_start: 0.7134 (mtp) cc_final: 0.6912 (mtp) REVERT: B 105 ASN cc_start: 0.8776 (m-40) cc_final: 0.8368 (t0) REVERT: B 111 MET cc_start: 0.6733 (mmm) cc_final: 0.6498 (mmm) REVERT: B 226 THR cc_start: 0.5500 (p) cc_final: 0.5186 (p) REVERT: B 343 MET cc_start: 0.7869 (ptp) cc_final: 0.7633 (ptp) REVERT: B 348 MET cc_start: 0.7115 (ttm) cc_final: 0.6216 (pmm) REVERT: B 372 MET cc_start: 0.7981 (ppp) cc_final: 0.7464 (tmm) REVERT: B 386 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7356 (tmm160) REVERT: B 439 ASP cc_start: 0.7879 (t0) cc_final: 0.7399 (t0) REVERT: B 545 GLN cc_start: 0.8147 (mt0) cc_final: 0.7870 (mt0) REVERT: B 581 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6698 (mm-30) REVERT: C 60 ASP cc_start: 0.8306 (p0) cc_final: 0.8075 (p0) REVERT: E 360 MET cc_start: 0.7088 (mmm) cc_final: 0.6873 (mmm) REVERT: E 438 ILE cc_start: 0.8254 (mp) cc_final: 0.7740 (tp) REVERT: E 460 MET cc_start: 0.7286 (mmt) cc_final: 0.6666 (mtt) REVERT: E 478 ASP cc_start: 0.8080 (p0) cc_final: 0.7659 (p0) REVERT: E 496 ARG cc_start: 0.5588 (ptp90) cc_final: 0.5234 (ptt180) REVERT: E 575 MET cc_start: 0.7053 (mtp) cc_final: 0.6817 (mtp) REVERT: F 87 CYS cc_start: 0.8352 (m) cc_final: 0.7958 (m) REVERT: F 105 ASN cc_start: 0.8740 (m-40) cc_final: 0.8230 (t0) REVERT: F 226 THR cc_start: 0.5511 (p) cc_final: 0.5157 (p) REVERT: F 372 MET cc_start: 0.7979 (ppp) cc_final: 0.7654 (tmm) REVERT: F 386 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7500 (ttm170) REVERT: F 439 ASP cc_start: 0.7955 (t0) cc_final: 0.7459 (t0) REVERT: F 545 GLN cc_start: 0.7603 (mt0) cc_final: 0.7330 (mt0) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.3125 time to fit residues: 216.2405 Evaluate side-chains 397 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 147 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.166953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140561 restraints weight = 102607.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145768 restraints weight = 51026.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149181 restraints weight = 31601.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151431 restraints weight = 22758.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152709 restraints weight = 18110.363| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20016 Z= 0.188 Angle : 0.635 24.677 27182 Z= 0.336 Chirality : 0.038 0.162 2992 Planarity : 0.005 0.056 3412 Dihedral : 10.131 80.457 2936 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.33 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.17), residues: 2360 helix: 0.10 (0.15), residues: 1058 sheet: -3.08 (0.35), residues: 192 loop : -2.21 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 443 TYR 0.022 0.001 TYR F 467 PHE 0.018 0.001 PHE E 520 TRP 0.010 0.001 TRP A 338 HIS 0.005 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00411 (20016) covalent geometry : angle 0.63456 (27182) hydrogen bonds : bond 0.05003 ( 817) hydrogen bonds : angle 5.48970 ( 2388) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8198 (mp) cc_final: 0.7568 (tp) REVERT: A 460 MET cc_start: 0.7330 (mmt) cc_final: 0.6719 (mtt) REVERT: A 496 ARG cc_start: 0.5952 (ptp90) cc_final: 0.5228 (ptt180) REVERT: A 523 MET cc_start: 0.8665 (mtt) cc_final: 0.8462 (mtt) REVERT: B 105 ASN cc_start: 0.8792 (m-40) cc_final: 0.8288 (t0) REVERT: B 111 MET cc_start: 0.6771 (mmm) cc_final: 0.6555 (mmm) REVERT: B 226 THR cc_start: 0.5348 (p) cc_final: 0.5004 (p) REVERT: B 343 MET cc_start: 0.7850 (ptp) cc_final: 0.7619 (ptp) REVERT: B 372 MET cc_start: 0.7959 (ppp) cc_final: 0.7542 (tmm) REVERT: B 386 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7516 (ttm170) REVERT: B 439 ASP cc_start: 0.7823 (t0) cc_final: 0.7393 (t0) REVERT: B 545 GLN cc_start: 0.8201 (mt0) cc_final: 0.7870 (mt0) REVERT: C 60 ASP cc_start: 0.8226 (p0) cc_final: 0.8006 (p0) REVERT: E 249 MET cc_start: 0.8078 (ttt) cc_final: 0.7461 (ttt) REVERT: E 358 LYS cc_start: 0.6983 (tptp) cc_final: 0.6622 (tptm) REVERT: E 438 ILE cc_start: 0.8234 (mp) cc_final: 0.7779 (tp) REVERT: E 460 MET cc_start: 0.7269 (mmt) cc_final: 0.6687 (mtt) REVERT: E 465 ILE cc_start: 0.8663 (mt) cc_final: 0.8346 (tt) REVERT: E 478 ASP cc_start: 0.8049 (p0) cc_final: 0.7623 (p0) REVERT: E 496 ARG cc_start: 0.5634 (ptp90) cc_final: 0.5143 (ptt180) REVERT: E 575 MET cc_start: 0.7213 (mtp) cc_final: 0.6978 (mtp) REVERT: F 87 CYS cc_start: 0.8382 (m) cc_final: 0.7967 (m) REVERT: F 105 ASN cc_start: 0.8746 (m-40) cc_final: 0.8217 (t0) REVERT: F 226 THR cc_start: 0.5514 (p) cc_final: 0.5162 (p) REVERT: F 372 MET cc_start: 0.7919 (ppp) cc_final: 0.7710 (tmm) REVERT: F 439 ASP cc_start: 0.7933 (t0) cc_final: 0.7450 (t0) REVERT: F 514 VAL cc_start: 0.8453 (m) cc_final: 0.7984 (p) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.3092 time to fit residues: 214.7671 Evaluate side-chains 394 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 108 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.163134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136390 restraints weight = 104012.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141526 restraints weight = 52570.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144921 restraints weight = 33013.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147128 restraints weight = 23919.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.148532 restraints weight = 19148.413| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 20016 Z= 0.279 Angle : 0.693 24.668 27182 Z= 0.371 Chirality : 0.041 0.162 2992 Planarity : 0.005 0.057 3412 Dihedral : 10.253 81.241 2936 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.11 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.17), residues: 2360 helix: -0.07 (0.15), residues: 1060 sheet: -3.21 (0.32), residues: 218 loop : -2.39 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 443 TYR 0.026 0.002 TYR F 467 PHE 0.025 0.002 PHE E 520 TRP 0.013 0.002 TRP E 537 HIS 0.007 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00617 (20016) covalent geometry : angle 0.69296 (27182) hydrogen bonds : bond 0.05285 ( 817) hydrogen bonds : angle 5.70500 ( 2388) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 449 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8240 (mp) cc_final: 0.7524 (tp) REVERT: A 460 MET cc_start: 0.7246 (mmt) cc_final: 0.6752 (mtt) REVERT: A 496 ARG cc_start: 0.5926 (ptp90) cc_final: 0.5253 (ptt180) REVERT: B 105 ASN cc_start: 0.8827 (m-40) cc_final: 0.8312 (t0) REVERT: B 110 THR cc_start: 0.9178 (p) cc_final: 0.8875 (p) REVERT: B 111 MET cc_start: 0.6820 (mmm) cc_final: 0.6556 (mmm) REVERT: B 226 THR cc_start: 0.5340 (p) cc_final: 0.5006 (p) REVERT: B 343 MET cc_start: 0.7933 (ptp) cc_final: 0.7678 (ptp) REVERT: B 372 MET cc_start: 0.8009 (ppp) cc_final: 0.7653 (tmm) REVERT: B 386 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7515 (ttm170) REVERT: B 439 ASP cc_start: 0.7897 (t0) cc_final: 0.7490 (t0) REVERT: B 545 GLN cc_start: 0.8261 (mt0) cc_final: 0.7918 (mt0) REVERT: C 60 ASP cc_start: 0.8308 (p0) cc_final: 0.8085 (p0) REVERT: E 358 LYS cc_start: 0.7033 (tptp) cc_final: 0.6697 (tptp) REVERT: E 438 ILE cc_start: 0.8357 (mp) cc_final: 0.7774 (tp) REVERT: E 460 MET cc_start: 0.7148 (mmt) cc_final: 0.6699 (mtt) REVERT: E 465 ILE cc_start: 0.8721 (mt) cc_final: 0.8428 (tt) REVERT: E 478 ASP cc_start: 0.8174 (p0) cc_final: 0.7755 (p0) REVERT: E 496 ARG cc_start: 0.5731 (ptp90) cc_final: 0.5103 (ptt180) REVERT: E 512 ARG cc_start: 0.6753 (mtp180) cc_final: 0.5619 (mmp-170) REVERT: F 87 CYS cc_start: 0.8380 (m) cc_final: 0.7888 (m) REVERT: F 105 ASN cc_start: 0.8783 (m-40) cc_final: 0.8224 (t0) REVERT: F 226 THR cc_start: 0.5581 (p) cc_final: 0.5226 (p) REVERT: F 403 LEU cc_start: 0.6655 (pt) cc_final: 0.6449 (pt) REVERT: F 439 ASP cc_start: 0.7927 (t0) cc_final: 0.7455 (t0) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.3200 time to fit residues: 217.0592 Evaluate side-chains 385 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 83 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 203 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN F 312 ASN ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 ASN F 664 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.168087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.141664 restraints weight = 102576.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.147007 restraints weight = 50691.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150474 restraints weight = 31198.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152780 restraints weight = 22327.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154112 restraints weight = 17616.593| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20016 Z= 0.136 Angle : 0.621 24.946 27182 Z= 0.325 Chirality : 0.038 0.164 2992 Planarity : 0.005 0.054 3412 Dihedral : 10.098 84.733 2936 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.03 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2360 helix: 0.28 (0.15), residues: 1058 sheet: -2.83 (0.35), residues: 194 loop : -2.26 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 443 TYR 0.020 0.001 TYR F 467 PHE 0.017 0.002 PHE E 710 TRP 0.014 0.001 TRP E 619 HIS 0.005 0.001 HIS F 664 Details of bonding type rmsd covalent geometry : bond 0.00309 (20016) covalent geometry : angle 0.62107 (27182) hydrogen bonds : bond 0.04813 ( 817) hydrogen bonds : angle 5.30232 ( 2388) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 438 ILE cc_start: 0.8097 (mp) cc_final: 0.7425 (tp) REVERT: A 460 MET cc_start: 0.7325 (mmt) cc_final: 0.6825 (mtt) REVERT: A 496 ARG cc_start: 0.5840 (ptp90) cc_final: 0.5254 (ptt180) REVERT: B 105 ASN cc_start: 0.8729 (m-40) cc_final: 0.8301 (t0) REVERT: B 226 THR cc_start: 0.5369 (p) cc_final: 0.5047 (p) REVERT: B 372 MET cc_start: 0.7771 (ppp) cc_final: 0.7508 (tmm) REVERT: B 386 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7411 (ttm170) REVERT: B 439 ASP cc_start: 0.7689 (t0) cc_final: 0.7356 (t0) REVERT: B 528 THR cc_start: 0.8943 (m) cc_final: 0.8707 (t) REVERT: C 60 ASP cc_start: 0.8257 (p0) cc_final: 0.8045 (p0) REVERT: E 313 THR cc_start: 0.7864 (m) cc_final: 0.7615 (m) REVERT: E 438 ILE cc_start: 0.8231 (mp) cc_final: 0.7650 (tp) REVERT: E 460 MET cc_start: 0.7240 (mmt) cc_final: 0.6758 (mtt) REVERT: E 478 ASP cc_start: 0.7996 (p0) cc_final: 0.7602 (p0) REVERT: E 496 ARG cc_start: 0.5880 (ptp90) cc_final: 0.5154 (ptt180) REVERT: E 512 ARG cc_start: 0.6723 (mtp180) cc_final: 0.5573 (mmp-170) REVERT: E 575 MET cc_start: 0.6933 (mtp) cc_final: 0.6725 (mtp) REVERT: F 87 CYS cc_start: 0.8334 (m) cc_final: 0.7876 (m) REVERT: F 105 ASN cc_start: 0.8729 (m-40) cc_final: 0.8245 (t0) REVERT: F 226 THR cc_start: 0.5512 (p) cc_final: 0.5187 (p) REVERT: F 372 MET cc_start: 0.7659 (ppp) cc_final: 0.7448 (tmm) REVERT: F 403 LEU cc_start: 0.6179 (pt) cc_final: 0.5928 (pt) REVERT: F 439 ASP cc_start: 0.7767 (t0) cc_final: 0.7385 (t0) REVERT: F 545 GLN cc_start: 0.7500 (mt0) cc_final: 0.7266 (mt0) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.2986 time to fit residues: 207.3178 Evaluate side-chains 393 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 8 optimal weight: 3.9990 chunk 177 optimal weight: 0.0000 chunk 185 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 222 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 382 ASN B 476 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.167187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140697 restraints weight = 102600.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146024 restraints weight = 51661.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149468 restraints weight = 31896.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151763 restraints weight = 22938.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.153148 restraints weight = 18173.346| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20016 Z= 0.163 Angle : 0.619 25.250 27182 Z= 0.325 Chirality : 0.038 0.164 2992 Planarity : 0.005 0.067 3412 Dihedral : 10.025 83.655 2936 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.75 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.17), residues: 2360 helix: 0.33 (0.15), residues: 1060 sheet: -2.82 (0.36), residues: 190 loop : -2.27 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 495 TYR 0.023 0.001 TYR F 467 PHE 0.015 0.001 PHE A 520 TRP 0.009 0.001 TRP F 666 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00364 (20016) covalent geometry : angle 0.61915 (27182) hydrogen bonds : bond 0.04764 ( 817) hydrogen bonds : angle 5.29827 ( 2388) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 438 ILE cc_start: 0.8141 (mp) cc_final: 0.7535 (tp) REVERT: A 460 MET cc_start: 0.7178 (mmt) cc_final: 0.6761 (mtt) REVERT: A 496 ARG cc_start: 0.5911 (ptp90) cc_final: 0.5254 (ptt180) REVERT: B 105 ASN cc_start: 0.8681 (m-40) cc_final: 0.8243 (t0) REVERT: B 124 GLN cc_start: 0.7530 (mp10) cc_final: 0.7068 (pp30) REVERT: B 226 THR cc_start: 0.5447 (p) cc_final: 0.5132 (p) REVERT: B 386 ARG cc_start: 0.7772 (mtm110) cc_final: 0.7407 (ttm170) REVERT: B 403 LEU cc_start: 0.6484 (pt) cc_final: 0.6264 (pt) REVERT: B 439 ASP cc_start: 0.7730 (t0) cc_final: 0.7381 (t0) REVERT: B 528 THR cc_start: 0.8963 (m) cc_final: 0.8701 (t) REVERT: C 60 ASP cc_start: 0.8245 (p0) cc_final: 0.8037 (p0) REVERT: E 313 THR cc_start: 0.7963 (m) cc_final: 0.7721 (m) REVERT: E 360 MET cc_start: 0.7137 (mmm) cc_final: 0.6804 (mmm) REVERT: E 438 ILE cc_start: 0.8301 (mp) cc_final: 0.7661 (tp) REVERT: E 460 MET cc_start: 0.7257 (mmt) cc_final: 0.6762 (mtt) REVERT: E 478 ASP cc_start: 0.7967 (p0) cc_final: 0.7721 (p0) REVERT: E 496 ARG cc_start: 0.5916 (ptp90) cc_final: 0.5152 (ptt180) REVERT: E 575 MET cc_start: 0.7028 (mtp) cc_final: 0.6823 (mtp) REVERT: F 87 CYS cc_start: 0.8361 (m) cc_final: 0.7912 (m) REVERT: F 105 ASN cc_start: 0.8726 (m-40) cc_final: 0.8197 (t0) REVERT: F 226 THR cc_start: 0.5451 (p) cc_final: 0.5139 (p) REVERT: F 372 MET cc_start: 0.7838 (ppp) cc_final: 0.7558 (tmm) REVERT: F 386 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7418 (ttm170) REVERT: F 403 LEU cc_start: 0.6155 (pt) cc_final: 0.5949 (pt) REVERT: F 439 ASP cc_start: 0.7837 (t0) cc_final: 0.7467 (t0) REVERT: F 545 GLN cc_start: 0.7561 (mt0) cc_final: 0.7268 (mt0) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.2984 time to fit residues: 203.9945 Evaluate side-chains 390 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 476 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.166877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.140286 restraints weight = 102783.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145650 restraints weight = 49817.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.149177 restraints weight = 30380.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151486 restraints weight = 21574.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153029 restraints weight = 16996.779| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20016 Z= 0.157 Angle : 0.616 25.196 27182 Z= 0.323 Chirality : 0.038 0.184 2992 Planarity : 0.005 0.052 3412 Dihedral : 9.973 84.147 2936 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.71 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2360 helix: 0.42 (0.16), residues: 1058 sheet: -2.76 (0.36), residues: 190 loop : -2.23 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 316 TYR 0.022 0.001 TYR F 467 PHE 0.017 0.001 PHE A 562 TRP 0.017 0.001 TRP F 666 HIS 0.005 0.001 HIS E 510 Details of bonding type rmsd covalent geometry : bond 0.00354 (20016) covalent geometry : angle 0.61634 (27182) hydrogen bonds : bond 0.04677 ( 817) hydrogen bonds : angle 5.21512 ( 2388) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 450 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 VAL cc_start: 0.8457 (t) cc_final: 0.8254 (t) REVERT: A 358 LYS cc_start: 0.6786 (tptp) cc_final: 0.6584 (tptp) REVERT: A 438 ILE cc_start: 0.8230 (mp) cc_final: 0.7551 (tp) REVERT: A 460 MET cc_start: 0.7214 (mmt) cc_final: 0.6801 (mtt) REVERT: A 496 ARG cc_start: 0.5927 (ptp90) cc_final: 0.5221 (ptt180) REVERT: B 105 ASN cc_start: 0.8727 (m-40) cc_final: 0.8314 (t0) REVERT: B 226 THR cc_start: 0.5450 (p) cc_final: 0.5138 (p) REVERT: B 372 MET cc_start: 0.7802 (ppp) cc_final: 0.7299 (tmm) REVERT: B 386 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7419 (ttm170) REVERT: B 403 LEU cc_start: 0.6509 (pt) cc_final: 0.6302 (pt) REVERT: B 439 ASP cc_start: 0.7767 (t0) cc_final: 0.7407 (t0) REVERT: B 528 THR cc_start: 0.8964 (m) cc_final: 0.8588 (t) REVERT: C 60 ASP cc_start: 0.8247 (p0) cc_final: 0.8040 (p0) REVERT: E 249 MET cc_start: 0.7753 (ttt) cc_final: 0.7427 (ttt) REVERT: E 313 THR cc_start: 0.8032 (m) cc_final: 0.7784 (m) REVERT: E 360 MET cc_start: 0.7148 (mmm) cc_final: 0.6846 (mmm) REVERT: E 438 ILE cc_start: 0.8357 (mp) cc_final: 0.7717 (tp) REVERT: E 460 MET cc_start: 0.7280 (mmt) cc_final: 0.6750 (mtt) REVERT: E 478 ASP cc_start: 0.7958 (p0) cc_final: 0.7747 (p0) REVERT: E 496 ARG cc_start: 0.5916 (ptp90) cc_final: 0.5184 (ptt180) REVERT: E 575 MET cc_start: 0.7106 (mtp) cc_final: 0.6836 (mtp) REVERT: F 87 CYS cc_start: 0.8427 (m) cc_final: 0.7936 (m) REVERT: F 105 ASN cc_start: 0.8742 (m-40) cc_final: 0.8213 (t0) REVERT: F 226 THR cc_start: 0.5415 (p) cc_final: 0.5104 (p) REVERT: F 372 MET cc_start: 0.7840 (ppp) cc_final: 0.7601 (tmm) REVERT: F 403 LEU cc_start: 0.6215 (pt) cc_final: 0.5979 (pt) REVERT: F 439 ASP cc_start: 0.7813 (t0) cc_final: 0.7471 (t0) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.2998 time to fit residues: 209.1687 Evaluate side-chains 388 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 147 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 476 ASN E 239 ASN E 591 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.166978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140656 restraints weight = 103095.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145929 restraints weight = 51125.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149427 restraints weight = 31640.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151680 restraints weight = 22515.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152957 restraints weight = 17833.486| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20016 Z= 0.154 Angle : 0.611 25.207 27182 Z= 0.321 Chirality : 0.038 0.164 2992 Planarity : 0.005 0.053 3412 Dihedral : 9.927 84.468 2936 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.75 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.17), residues: 2360 helix: 0.49 (0.16), residues: 1054 sheet: -2.74 (0.37), residues: 190 loop : -2.12 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 495 TYR 0.020 0.001 TYR F 467 PHE 0.015 0.001 PHE E 562 TRP 0.025 0.001 TRP F 666 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00340 (20016) covalent geometry : angle 0.61099 (27182) hydrogen bonds : bond 0.04636 ( 817) hydrogen bonds : angle 5.19426 ( 2388) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8235 (mp) cc_final: 0.7542 (tp) REVERT: A 460 MET cc_start: 0.7166 (mmt) cc_final: 0.6747 (mtt) REVERT: A 496 ARG cc_start: 0.5869 (ptp90) cc_final: 0.5210 (ptt180) REVERT: A 661 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6696 (mm-30) REVERT: B 105 ASN cc_start: 0.8748 (m-40) cc_final: 0.8328 (t0) REVERT: B 226 THR cc_start: 0.5400 (p) cc_final: 0.5104 (p) REVERT: B 372 MET cc_start: 0.7808 (ppp) cc_final: 0.7400 (tmm) REVERT: B 386 ARG cc_start: 0.7757 (mtm110) cc_final: 0.7387 (ttm170) REVERT: B 403 LEU cc_start: 0.6502 (pt) cc_final: 0.6255 (pt) REVERT: B 439 ASP cc_start: 0.7753 (t0) cc_final: 0.7450 (t0) REVERT: B 528 THR cc_start: 0.8986 (m) cc_final: 0.8588 (t) REVERT: C 60 ASP cc_start: 0.8386 (p0) cc_final: 0.8141 (p0) REVERT: E 223 PHE cc_start: 0.7345 (m-80) cc_final: 0.7121 (m-10) REVERT: E 313 THR cc_start: 0.8014 (m) cc_final: 0.7771 (m) REVERT: E 360 MET cc_start: 0.7108 (mmm) cc_final: 0.6757 (mmm) REVERT: E 438 ILE cc_start: 0.8359 (mp) cc_final: 0.7655 (tp) REVERT: E 460 MET cc_start: 0.7284 (mmt) cc_final: 0.6772 (mtt) REVERT: E 478 ASP cc_start: 0.7957 (p0) cc_final: 0.7731 (p0) REVERT: E 496 ARG cc_start: 0.5930 (ptp90) cc_final: 0.5196 (ptt180) REVERT: E 575 MET cc_start: 0.7097 (mtp) cc_final: 0.6805 (mtp) REVERT: F 87 CYS cc_start: 0.8400 (m) cc_final: 0.7928 (m) REVERT: F 105 ASN cc_start: 0.8732 (m-40) cc_final: 0.8238 (t0) REVERT: F 226 THR cc_start: 0.5397 (p) cc_final: 0.5109 (p) REVERT: F 372 MET cc_start: 0.7787 (ppp) cc_final: 0.7585 (tmm) REVERT: F 403 LEU cc_start: 0.6233 (pt) cc_final: 0.6003 (pt) REVERT: F 439 ASP cc_start: 0.7753 (t0) cc_final: 0.7436 (t0) REVERT: F 491 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7325 (tt0) REVERT: F 545 GLN cc_start: 0.7690 (mt0) cc_final: 0.7471 (mt0) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.3039 time to fit residues: 210.7714 Evaluate side-chains 397 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 151 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 74 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 476 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 ASN ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.165756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140128 restraints weight = 100937.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145350 restraints weight = 50396.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148746 restraints weight = 30879.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.151005 restraints weight = 21933.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152392 restraints weight = 17301.555| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20016 Z= 0.162 Angle : 0.620 25.211 27182 Z= 0.326 Chirality : 0.038 0.166 2992 Planarity : 0.005 0.052 3412 Dihedral : 9.909 84.633 2936 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.58 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.17), residues: 2360 helix: 0.50 (0.16), residues: 1054 sheet: -2.73 (0.37), residues: 190 loop : -2.11 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 495 TYR 0.022 0.001 TYR F 467 PHE 0.015 0.002 PHE E 520 TRP 0.021 0.001 TRP F 666 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00365 (20016) covalent geometry : angle 0.62012 (27182) hydrogen bonds : bond 0.04612 ( 817) hydrogen bonds : angle 5.19885 ( 2388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6222.17 seconds wall clock time: 106 minutes 58.59 seconds (6418.59 seconds total)