Starting phenix.real_space_refine on Sat Mar 7 08:46:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qxe_4666/03_2026/6qxe_4666.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qxe_4666/03_2026/6qxe_4666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qxe_4666/03_2026/6qxe_4666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qxe_4666/03_2026/6qxe_4666.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qxe_4666/03_2026/6qxe_4666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qxe_4666/03_2026/6qxe_4666.map" } resolution = 4.15 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 146 5.16 5 C 13434 2.51 5 N 3700 2.21 5 O 4106 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 54 residue(s): 0.02s 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: 40460 Number of models: 1 Model: "" Number of chains: 10 Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "O" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} 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: 7.14, per 1000 atoms: 0.18 Number of scatterers: 40460 At special positions: 0 Unit cell: (186.84, 113.4, 102.6, 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 146 16.00 P 24 15.00 O 4106 8.00 N 3700 7.00 C 13434 6.00 H 19050 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 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: 3.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4916 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 20 sheets defined 45.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.706A pdb=" N ASN M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.690A pdb=" N ASN O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.645A pdb=" N SER O 91 " --> pdb=" O PRO O 88 " (cutoff:3.500A) 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: 3.631A 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: 4.049A 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: 4.571A 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: 4.512A 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: 3.689A 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: 4.659A 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: 3.834A 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: 4.024A 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: 3.741A 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: 4.583A 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: 3.560A 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: 4.105A 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: 3.747A 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: 4.047A 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: 3.689A 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: 3.564A 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: 3.678A 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: 3.742A pdb=" N GLN F 313 " --> pdb=" O TRP F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.817A 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: 3.796A 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: 3.794A 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: 3.998A 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: 3.623A pdb=" N LEU G 125 " --> pdb=" O LYS G 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.412A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET M 34 " --> pdb=" O MET M 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.522A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET O 34 " --> pdb=" O MET O 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA6, 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: 6.584A 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=AA7, 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=AA8, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA9, 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=AB1, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.717A pdb=" N ILE B 397 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 400 " --> pdb=" O ILE B 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 441 removed outlier: 3.619A pdb=" N TRP B 437 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 441 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing sheet with id=AB3, 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: 3.651A pdb=" N ALA C 59 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 390 through 391 Processing sheet with id=AB5, 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: 4.184A 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: 3.888A 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: 5.575A pdb=" N GLU E 544 " --> pdb=" O LEU E 563 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL E 565 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL E 542 " --> pdb=" O VAL E 565 " (cutoff:3.500A) Processing sheet with id=AB6, 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=AB7, first strand: chain 'F' and resid 55 through 57 Processing sheet with id=AB8, first strand: chain 'F' and resid 128 through 130 removed outlier: 3.511A 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=AB9, 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=AB9 Processing sheet with id=AC1, 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=AC2, 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) 880 hydrogen bonds defined for protein. 2538 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: 8.47 Time building geometry restraints manager: 5.15 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: 3534 1.28 - 1.55: 18102 1.55 - 1.82: 326 Warning: very small bond lengths. Bond restraints: 40974 Sorted by residual: bond pdb=" N2 G H 12 " pdb=" H21 G H 12 " ideal model delta sigma weight residual 0.860 0.468 0.392 2.00e-02 2.50e+03 3.85e+02 bond pdb=" N2 G D 12 " pdb=" H21 G D 12 " ideal model delta sigma weight residual 0.860 0.473 0.387 2.00e-02 2.50e+03 3.75e+02 bond pdb=" ND2 ASN F 532 " pdb="HD22 ASN F 532 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+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 3.62e+01 bond pdb=" NZ LYS F 531 " pdb=" HZ3 LYS F 531 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 40969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 23.66: 73138 23.66 - 47.31: 1 47.31 - 70.97: 3 70.97 - 94.62: 0 94.62 - 118.28: 2 Bond angle restraints: 73144 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 1.72 118.28 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 4.43 115.57 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 58.66 55.61 3.00e+00 1.11e-01 3.44e+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 69.24 55.33 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 74.28 50.27 3.00e+00 1.11e-01 2.81e+02 ... (remaining 73139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 16829 17.66 - 35.33: 2059 35.33 - 52.99: 474 52.99 - 70.66: 137 70.66 - 88.32: 33 Dihedral angle restraints: 19532 sinusoidal: 10730 harmonic: 8802 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 180.00 151.93 28.07 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 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LEU A 283 " pdb=" C LEU A 283 " pdb=" N LEU A 284 " pdb=" CA LEU A 284 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 19529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2823 0.067 - 0.134: 398 0.134 - 0.200: 36 0.200 - 0.267: 3 0.267 - 0.334: 2 Chirality restraints: 3262 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 2.70e+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 2.28 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3259 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 514 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" N SER B 515 " 0.066 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 3.83e-02 1.46e+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 3.81e-02 1.45e+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 6021 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.55: 11 1.55 - 2.31: 11174 2.31 - 3.07: 121080 3.07 - 3.84: 161295 3.84 - 4.60: 265198 Warning: very small nonbonded interaction distances. Nonbonded interactions: 558758 Sorted by model distance: nonbonded pdb=" CD LYS M 43 " pdb="HG13 ILE A 554 " model vdw 0.787 2.920 nonbonded pdb=" HE1 TYR F 24 " pdb=" HG3 PRO F 28 " model vdw 1.268 2.270 nonbonded pdb=" CH2 TRP O 105 " pdb="HH22 ARG B 563 " model vdw 1.277 2.800 nonbonded pdb=" O ALA M 56 " pdb=" HB3 GLU E 427 " model vdw 1.334 2.620 nonbonded pdb=" CH2 TRP M 105 " pdb="HH22 ARG F 563 " model vdw 1.392 2.800 ... (remaining 558753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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' } ncs_group { reference = chain 'M' selection = chain 'O' } 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: 0.920 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: 0.230 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 35.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 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 21926 Z= 0.352 Angle : 0.917 19.639 29772 Z= 0.508 Chirality : 0.047 0.334 3262 Planarity : 0.007 0.085 3750 Dihedral : 15.347 88.320 8374 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.54 % Favored : 92.30 % Rotamer: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.10 % 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: -3.74 (0.14), residues: 2598 helix: -1.90 (0.13), residues: 1046 sheet: -3.03 (0.27), residues: 274 loop : -2.86 (0.16), residues: 1278 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 0.002 TRP A 577 HIS 0.008 0.002 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00784 (21924) covalent geometry : angle 0.91738 (29768) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.65479 ( 4) hydrogen bonds : bond 0.17205 ( 880) hydrogen bonds : angle 7.45386 ( 2538) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 704 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 701 time to evaluate : 1.039 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 30 SER cc_start: 0.8624 (t) cc_final: 0.8373 (p) REVERT: M 31 ASN cc_start: 0.7393 (m-40) cc_final: 0.6722 (m-40) REVERT: A 356 ARG cc_start: 0.6616 (mtt180) cc_final: 0.6278 (mtt90) REVERT: A 450 VAL cc_start: 0.7605 (t) cc_final: 0.7298 (p) REVERT: A 557 MET cc_start: 0.6955 (mmp) cc_final: 0.6113 (mmt) REVERT: B 246 MET cc_start: 0.4954 (ptm) cc_final: 0.4477 (tpp) REVERT: B 501 PHE cc_start: 0.5904 (t80) cc_final: 0.5506 (t80) REVERT: B 576 LEU cc_start: 0.7250 (mt) cc_final: 0.6954 (mt) REVERT: E 431 ASP cc_start: 0.7627 (p0) cc_final: 0.7402 (p0) REVERT: E 568 ASN cc_start: 0.6682 (t0) cc_final: 0.6196 (m-40) REVERT: E 667 LEU cc_start: 0.7330 (tp) cc_final: 0.6979 (tt) REVERT: F 432 THR cc_start: 0.6553 (t) cc_final: 0.6124 (m) REVERT: F 483 TYR cc_start: 0.5400 (p90) cc_final: 0.4660 (p90) REVERT: G 81 MET cc_start: 0.6460 (mtm) cc_final: 0.5215 (mmp) outliers start: 3 outliers final: 0 residues processed: 704 average time/residue: 0.3889 time to fit residues: 401.8386 Evaluate side-chains 428 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 31 ASN O 31 ASN O 54 ASN A 278 GLN A 333 ASN A 383 ASN A 535 HIS B 664 HIS E 383 ASN E 513 ASN E 675 ASN F 382 ASN F 428 GLN F 485 ASN F 533 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.199940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.174076 restraints weight = 121600.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.176050 restraints weight = 68489.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.176883 restraints weight = 52550.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.178102 restraints weight = 44819.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.177815 restraints weight = 38419.865| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21926 Z= 0.175 Angle : 0.695 24.395 29772 Z= 0.371 Chirality : 0.041 0.201 3262 Planarity : 0.006 0.077 3750 Dihedral : 10.068 84.626 3206 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.11 % 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 (0.15), residues: 2598 helix: -0.80 (0.14), residues: 1074 sheet: -2.63 (0.28), residues: 288 loop : -2.64 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 512 TYR 0.021 0.002 TYR M 114 PHE 0.026 0.002 PHE B 166 TRP 0.030 0.002 TRP B 332 HIS 0.009 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00382 (21924) covalent geometry : angle 0.69529 (29768) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.66488 ( 4) hydrogen bonds : bond 0.05667 ( 880) hydrogen bonds : angle 6.09638 ( 2538) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 500 time to evaluate : 1.082 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 34 MET cc_start: 0.6802 (mtt) cc_final: 0.6523 (mpp) REVERT: O 57 ASP cc_start: 0.6556 (t0) cc_final: 0.5997 (t70) REVERT: O 73 ASP cc_start: 0.5943 (t0) cc_final: 0.5341 (m-30) REVERT: O 83 MET cc_start: 0.7351 (mtp) cc_final: 0.7062 (mtm) REVERT: O 104 ILE cc_start: 0.7038 (mp) cc_final: 0.6728 (mt) REVERT: A 276 CYS cc_start: 0.8830 (m) cc_final: 0.8620 (m) REVERT: A 327 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6309 (tp30) REVERT: A 396 ASP cc_start: 0.4743 (t0) cc_final: 0.4486 (t70) REVERT: A 470 LEU cc_start: 0.8806 (tp) cc_final: 0.8552 (tp) REVERT: B 1 MET cc_start: 0.5836 (tpp) cc_final: 0.5503 (tpp) REVERT: B 244 PRO cc_start: 0.5484 (Cg_endo) cc_final: 0.4808 (Cg_exo) REVERT: B 246 MET cc_start: 0.5580 (ptm) cc_final: 0.4861 (tpp) REVERT: B 576 LEU cc_start: 0.7401 (mt) cc_final: 0.6960 (mt) REVERT: E 285 MET cc_start: 0.5891 (pmm) cc_final: 0.5489 (ptt) REVERT: E 427 GLU cc_start: 0.5118 (pp20) cc_final: 0.4242 (pp20) REVERT: E 562 PHE cc_start: 0.7481 (m-10) cc_final: 0.7232 (m-10) REVERT: E 568 ASN cc_start: 0.7732 (t0) cc_final: 0.7111 (m-40) REVERT: F 122 LEU cc_start: 0.7845 (pp) cc_final: 0.7589 (tt) REVERT: F 483 TYR cc_start: 0.6185 (p90) cc_final: 0.5513 (p90) REVERT: F 616 MET cc_start: 0.6312 (mtp) cc_final: 0.6017 (mtp) REVERT: G 69 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6590 (tm-30) REVERT: G 81 MET cc_start: 0.6129 (mtm) cc_final: 0.5425 (mmp) outliers start: 3 outliers final: 1 residues processed: 502 average time/residue: 0.3504 time to fit residues: 267.8066 Evaluate side-chains 405 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 404 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 1 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 74 ASN A 239 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 591 GLN A 614 ASN B 67 ASN B 276 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS E 239 ASN ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 HIS F 65 GLN F 67 ASN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN F 382 ASN F 485 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.178586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.144829 restraints weight = 118643.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.144653 restraints weight = 76878.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146509 restraints weight = 58089.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148555 restraints weight = 46199.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148544 restraints weight = 41433.009| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.153 21926 Z= 0.292 Angle : 0.816 24.814 29772 Z= 0.437 Chirality : 0.044 0.207 3262 Planarity : 0.007 0.079 3750 Dihedral : 10.064 85.970 3206 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.78 % Favored : 91.11 % Rotamer: Outliers : 0.31 % Allowed : 4.99 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.57 (0.15), residues: 2598 helix: -0.49 (0.15), residues: 1054 sheet: -2.48 (0.30), residues: 256 loop : -2.64 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 162 TYR 0.022 0.003 TYR A 650 PHE 0.038 0.003 PHE A 236 TRP 0.029 0.002 TRP A 577 HIS 0.009 0.002 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00664 (21924) covalent geometry : angle 0.81584 (29768) SS BOND : bond 0.00274 ( 2) SS BOND : angle 1.18636 ( 4) hydrogen bonds : bond 0.06276 ( 880) hydrogen bonds : angle 6.03949 ( 2538) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 485 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 478 time to evaluate : 1.130 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 GLN cc_start: 0.8668 (pp30) cc_final: 0.8407 (pp30) REVERT: M 50 MET cc_start: 0.6296 (mtt) cc_final: 0.5949 (mtm) REVERT: A 465 ILE cc_start: 0.8291 (mt) cc_final: 0.8039 (mt) REVERT: A 557 MET cc_start: 0.8093 (mmm) cc_final: 0.7707 (mmp) REVERT: B 246 MET cc_start: 0.6500 (ptm) cc_final: 0.5378 (mmt) REVERT: B 282 LEU cc_start: 0.8138 (tt) cc_final: 0.7772 (mm) REVERT: B 324 TYR cc_start: 0.7727 (t80) cc_final: 0.7379 (t80) REVERT: B 501 PHE cc_start: 0.6286 (t80) cc_final: 0.5209 (t80) REVERT: C 65 GLU cc_start: 0.7048 (pm20) cc_final: 0.6475 (tm-30) REVERT: E 245 LYS cc_start: 0.6668 (mmtt) cc_final: 0.6413 (mmtp) REVERT: E 327 GLU cc_start: 0.6130 (mm-30) cc_final: 0.5870 (mm-30) REVERT: E 407 ILE cc_start: 0.8761 (tt) cc_final: 0.8527 (tp) REVERT: E 566 ARG cc_start: 0.7360 (ptm-80) cc_final: 0.7090 (ptm160) REVERT: E 568 ASN cc_start: 0.9243 (t0) cc_final: 0.8755 (m-40) REVERT: F 122 LEU cc_start: 0.8099 (pp) cc_final: 0.7747 (tt) REVERT: F 362 MET cc_start: 0.6912 (ptt) cc_final: 0.6301 (ppp) REVERT: G 81 MET cc_start: 0.6519 (mtm) cc_final: 0.5720 (mmp) outliers start: 7 outliers final: 2 residues processed: 483 average time/residue: 0.3583 time to fit residues: 261.6096 Evaluate side-chains 383 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 157 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 173 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 218 optimal weight: 0.0980 chunk 197 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 53 ASN M 77 ASN O 85 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.178762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.144080 restraints weight = 118088.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.145102 restraints weight = 78282.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147689 restraints weight = 55418.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148655 restraints weight = 41875.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148938 restraints weight = 40347.574| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21926 Z= 0.158 Angle : 0.636 25.575 29772 Z= 0.339 Chirality : 0.039 0.163 3262 Planarity : 0.005 0.064 3750 Dihedral : 9.877 84.797 3206 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.12 % Favored : 92.73 % Rotamer: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.15), residues: 2598 helix: -0.03 (0.15), residues: 1054 sheet: -2.31 (0.31), residues: 256 loop : -2.54 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 121 TYR 0.013 0.002 TYR B 129 PHE 0.027 0.002 PHE B 512 TRP 0.026 0.002 TRP O 105 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00353 (21924) covalent geometry : angle 0.63643 (29768) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.40326 ( 4) hydrogen bonds : bond 0.05303 ( 880) hydrogen bonds : angle 5.60448 ( 2538) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 454 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 1.160 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 GLN cc_start: 0.8736 (pp30) cc_final: 0.8444 (pp30) REVERT: O 50 MET cc_start: 0.7218 (mtm) cc_final: 0.6663 (mtp) REVERT: A 365 GLN cc_start: 0.7709 (mp10) cc_final: 0.7407 (mp10) REVERT: A 460 MET cc_start: 0.7878 (mmt) cc_final: 0.7456 (mmt) REVERT: A 465 ILE cc_start: 0.8144 (mt) cc_final: 0.7937 (mt) REVERT: A 557 MET cc_start: 0.8054 (mmm) cc_final: 0.7811 (mmp) REVERT: B 246 MET cc_start: 0.6612 (ptm) cc_final: 0.5406 (mmt) REVERT: B 282 LEU cc_start: 0.8089 (tt) cc_final: 0.7779 (mm) REVERT: B 324 TYR cc_start: 0.7784 (t80) cc_final: 0.7403 (t80) REVERT: B 565 ASP cc_start: 0.8174 (p0) cc_final: 0.7943 (p0) REVERT: C 65 GLU cc_start: 0.6929 (pm20) cc_final: 0.6463 (tm-30) REVERT: E 211 MET cc_start: 0.7521 (tmm) cc_final: 0.6826 (tmm) REVERT: F 408 MET cc_start: 0.7362 (mmm) cc_final: 0.6807 (mmm) REVERT: G 81 MET cc_start: 0.6504 (mtm) cc_final: 0.5744 (mmp) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.3434 time to fit residues: 239.5577 Evaluate side-chains 374 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 128 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 GLN B 16 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN F 67 ASN F 99 HIS F 313 GLN F 413 ASN F 485 ASN F 664 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.166421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.130266 restraints weight = 117040.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.130724 restraints weight = 84944.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132572 restraints weight = 65347.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133811 restraints weight = 50980.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133860 restraints weight = 47364.066| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 21926 Z= 0.266 Angle : 0.760 25.680 29772 Z= 0.410 Chirality : 0.043 0.244 3262 Planarity : 0.006 0.085 3750 Dihedral : 9.979 85.245 3206 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.16 % Favored : 89.68 % Rotamer: Outliers : 0.13 % Allowed : 4.33 % Favored : 95.54 % 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: -2.34 (0.15), residues: 2598 helix: -0.18 (0.15), residues: 1056 sheet: -1.91 (0.32), residues: 248 loop : -2.75 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 496 TYR 0.022 0.002 TYR F 620 PHE 0.048 0.003 PHE F 150 TRP 0.023 0.002 TRP E 577 HIS 0.012 0.002 HIS F 664 Details of bonding type rmsd covalent geometry : bond 0.00602 (21924) covalent geometry : angle 0.76026 (29768) SS BOND : bond 0.00444 ( 2) SS BOND : angle 1.15795 ( 4) hydrogen bonds : bond 0.05873 ( 880) hydrogen bonds : angle 5.83667 ( 2538) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 410 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 407 time to evaluate : 1.123 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: M 50 MET cc_start: 0.6640 (mtt) cc_final: 0.6323 (mtp) REVERT: O 11 MET cc_start: 0.7605 (ppp) cc_final: 0.7317 (ppp) REVERT: O 39 GLN cc_start: 0.7465 (tt0) cc_final: 0.6525 (tm-30) REVERT: O 50 MET cc_start: 0.7593 (mtm) cc_final: 0.7352 (mtp) REVERT: A 460 MET cc_start: 0.8121 (mmt) cc_final: 0.7467 (mmt) REVERT: A 557 MET cc_start: 0.8041 (mmm) cc_final: 0.7712 (mmt) REVERT: A 599 GLU cc_start: 0.7486 (tp30) cc_final: 0.6837 (tm-30) REVERT: B 109 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8511 (tp30) REVERT: B 246 MET cc_start: 0.6687 (ptm) cc_final: 0.5473 (mmt) REVERT: B 324 TYR cc_start: 0.7791 (t80) cc_final: 0.7438 (t80) REVERT: B 565 ASP cc_start: 0.8326 (p0) cc_final: 0.8102 (p0) REVERT: C 65 GLU cc_start: 0.6920 (pm20) cc_final: 0.6650 (tm-30) REVERT: E 524 GLU cc_start: 0.8503 (mp0) cc_final: 0.8136 (mp0) REVERT: E 661 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7378 (mp0) REVERT: E 672 LEU cc_start: 0.9011 (tp) cc_final: 0.8783 (tp) REVERT: F 24 TYR cc_start: 0.5577 (t80) cc_final: 0.5085 (t80) REVERT: F 362 MET cc_start: 0.6828 (ptt) cc_final: 0.6015 (ppp) REVERT: G 81 MET cc_start: 0.6724 (mtm) cc_final: 0.6064 (mmm) outliers start: 3 outliers final: 0 residues processed: 410 average time/residue: 0.3481 time to fit residues: 218.5415 Evaluate side-chains 332 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 177 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN M 77 ASN O 74 ASN O 85 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 44 ASN F 382 ASN F 425 ASN G 75 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.168872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133536 restraints weight = 117327.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.133945 restraints weight = 87802.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135069 restraints weight = 66981.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136156 restraints weight = 56148.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136419 restraints weight = 49253.215| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.8062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21926 Z= 0.143 Angle : 0.621 25.516 29772 Z= 0.331 Chirality : 0.039 0.202 3262 Planarity : 0.005 0.062 3750 Dihedral : 9.764 82.405 3206 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 0.22 % Allowed : 1.66 % Favored : 98.12 % 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: -1.87 (0.16), residues: 2598 helix: 0.36 (0.15), residues: 1048 sheet: -1.83 (0.33), residues: 228 loop : -2.57 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 100 TYR 0.020 0.002 TYR A 445 PHE 0.020 0.002 PHE B 512 TRP 0.025 0.001 TRP O 36 HIS 0.004 0.001 HIS F 664 Details of bonding type rmsd covalent geometry : bond 0.00318 (21924) covalent geometry : angle 0.62052 (29768) SS BOND : bond 0.00227 ( 2) SS BOND : angle 1.04066 ( 4) hydrogen bonds : bond 0.05217 ( 880) hydrogen bonds : angle 5.44794 ( 2538) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 409 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 404 time to evaluate : 1.132 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: O 39 GLN cc_start: 0.7163 (tt0) cc_final: 0.6619 (tm-30) REVERT: A 460 MET cc_start: 0.7741 (mmt) cc_final: 0.7353 (mmt) REVERT: A 557 MET cc_start: 0.8023 (mmm) cc_final: 0.7735 (mmt) REVERT: B 324 TYR cc_start: 0.7799 (t80) cc_final: 0.7454 (t80) REVERT: B 348 MET cc_start: 0.7576 (ttp) cc_final: 0.7114 (pmm) REVERT: B 424 LEU cc_start: 0.8692 (mt) cc_final: 0.8457 (mt) REVERT: B 565 ASP cc_start: 0.8283 (p0) cc_final: 0.7992 (p0) REVERT: C 123 GLU cc_start: 0.6463 (pp20) cc_final: 0.6221 (pp20) REVERT: E 211 MET cc_start: 0.7465 (tmm) cc_final: 0.6954 (tmm) REVERT: E 672 LEU cc_start: 0.9100 (tp) cc_final: 0.8847 (tp) REVERT: F 15 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: F 362 MET cc_start: 0.6800 (ptt) cc_final: 0.5985 (ppp) REVERT: G 81 MET cc_start: 0.6847 (mtm) cc_final: 0.6087 (mmm) outliers start: 5 outliers final: 2 residues processed: 408 average time/residue: 0.3393 time to fit residues: 215.1657 Evaluate side-chains 322 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 319 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 190 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN F 425 ASN G 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.164663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129663 restraints weight = 117727.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.131796 restraints weight = 98580.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133634 restraints weight = 67237.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133216 restraints weight = 51174.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.133525 restraints weight = 52217.590| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.8509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 21926 Z= 0.198 Angle : 0.651 25.452 29772 Z= 0.349 Chirality : 0.040 0.172 3262 Planarity : 0.006 0.107 3750 Dihedral : 9.752 82.389 3206 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.28 % Favored : 90.61 % Rotamer: Outliers : 0.04 % Allowed : 1.27 % Favored : 98.69 % 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: -1.86 (0.16), residues: 2598 helix: 0.39 (0.15), residues: 1044 sheet: -1.68 (0.33), residues: 240 loop : -2.61 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 121 TYR 0.018 0.002 TYR E 305 PHE 0.033 0.002 PHE B 333 TRP 0.022 0.002 TRP E 619 HIS 0.004 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00449 (21924) covalent geometry : angle 0.65109 (29768) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.93583 ( 4) hydrogen bonds : bond 0.05310 ( 880) hydrogen bonds : angle 5.47447 ( 2538) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 373 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 1.117 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: O 39 GLN cc_start: 0.7053 (tt0) cc_final: 0.6574 (tm-30) REVERT: A 460 MET cc_start: 0.7888 (mmt) cc_final: 0.7597 (mmt) REVERT: A 465 ILE cc_start: 0.8340 (mt) cc_final: 0.8118 (mt) REVERT: A 557 MET cc_start: 0.7934 (mmm) cc_final: 0.7408 (mmt) REVERT: B 324 TYR cc_start: 0.7659 (t80) cc_final: 0.7351 (t80) REVERT: C 66 MET cc_start: 0.6866 (mtp) cc_final: 0.6493 (mtp) REVERT: E 211 MET cc_start: 0.7231 (tmm) cc_final: 0.6872 (tmm) REVERT: E 672 LEU cc_start: 0.9168 (tp) cc_final: 0.8848 (tt) REVERT: G 81 MET cc_start: 0.6774 (mtm) cc_final: 0.6040 (mmm) outliers start: 1 outliers final: 1 residues processed: 373 average time/residue: 0.3312 time to fit residues: 190.3909 Evaluate side-chains 310 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 7 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN A 412 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN F 382 ASN F 425 ASN F 664 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.156495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121542 restraints weight = 118979.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119921 restraints weight = 101638.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121894 restraints weight = 85520.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122372 restraints weight = 66554.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122619 restraints weight = 55458.070| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.9497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 21926 Z= 0.314 Angle : 0.772 25.534 29772 Z= 0.423 Chirality : 0.044 0.323 3262 Planarity : 0.007 0.093 3750 Dihedral : 10.030 83.979 3206 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.05 % Favored : 88.84 % Rotamer: Outliers : 0.09 % Allowed : 1.31 % Favored : 98.60 % 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: -2.23 (0.16), residues: 2598 helix: 0.04 (0.15), residues: 1036 sheet: -1.67 (0.33), residues: 240 loop : -2.82 (0.15), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 100 TYR 0.027 0.002 TYR F 49 PHE 0.022 0.003 PHE F 9 TRP 0.025 0.003 TRP E 577 HIS 0.009 0.002 HIS F 664 Details of bonding type rmsd covalent geometry : bond 0.00713 (21924) covalent geometry : angle 0.77232 (29768) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.02672 ( 4) hydrogen bonds : bond 0.06161 ( 880) hydrogen bonds : angle 6.02012 ( 2538) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 350 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 1.152 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: O 39 GLN cc_start: 0.7243 (tt0) cc_final: 0.6535 (tm-30) REVERT: O 87 LYS cc_start: 0.8650 (mttt) cc_final: 0.8372 (mmtt) REVERT: A 297 HIS cc_start: 0.7995 (p-80) cc_final: 0.7734 (p-80) REVERT: A 460 MET cc_start: 0.8088 (mmt) cc_final: 0.7801 (mmt) REVERT: A 557 MET cc_start: 0.7971 (mmm) cc_final: 0.7462 (mmt) REVERT: A 605 LYS cc_start: 0.7707 (mttp) cc_final: 0.7333 (mtpt) REVERT: B 109 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8419 (tp30) REVERT: B 246 MET cc_start: 0.7072 (ptp) cc_final: 0.6726 (ptp) REVERT: B 249 ARG cc_start: 0.7031 (tpp-160) cc_final: 0.6547 (ttm170) REVERT: B 424 LEU cc_start: 0.9047 (mt) cc_final: 0.8825 (mt) REVERT: E 211 MET cc_start: 0.7611 (tmm) cc_final: 0.7350 (tmm) REVERT: E 693 CYS cc_start: 0.8644 (m) cc_final: 0.8127 (m) REVERT: F 318 PHE cc_start: 0.8201 (m-80) cc_final: 0.7367 (m-80) REVERT: G 60 ASP cc_start: 0.7994 (p0) cc_final: 0.7741 (p0) REVERT: G 81 MET cc_start: 0.7177 (mtm) cc_final: 0.6353 (mmm) outliers start: 2 outliers final: 1 residues processed: 350 average time/residue: 0.3212 time to fit residues: 175.7905 Evaluate side-chains 286 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 182 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS B 44 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN F 310 ASN F 335 ASN F 382 ASN F 425 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.160586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127608 restraints weight = 122740.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125894 restraints weight = 108267.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126958 restraints weight = 90823.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127657 restraints weight = 77776.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128039 restraints weight = 66297.725| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.9873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21926 Z= 0.213 Angle : 0.676 25.473 29772 Z= 0.366 Chirality : 0.041 0.186 3262 Planarity : 0.006 0.097 3750 Dihedral : 9.900 82.298 3206 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.24 % Favored : 90.61 % Rotamer: Outliers : 0.13 % Allowed : 0.66 % Favored : 99.21 % 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 (0.16), residues: 2598 helix: 0.26 (0.16), residues: 1044 sheet: -1.68 (0.33), residues: 240 loop : -2.70 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 260 TYR 0.021 0.002 TYR E 305 PHE 0.030 0.002 PHE F 318 TRP 0.036 0.002 TRP F 332 HIS 0.005 0.001 HIS F 664 Details of bonding type rmsd covalent geometry : bond 0.00482 (21924) covalent geometry : angle 0.67580 (29768) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.65718 ( 4) hydrogen bonds : bond 0.05769 ( 880) hydrogen bonds : angle 5.63102 ( 2538) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 353 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 1.141 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: O 27 PHE cc_start: 0.7477 (p90) cc_final: 0.7195 (p90) REVERT: O 39 GLN cc_start: 0.7055 (tt0) cc_final: 0.6567 (tm-30) REVERT: O 87 LYS cc_start: 0.8595 (mttt) cc_final: 0.8391 (mmtt) REVERT: A 460 MET cc_start: 0.7911 (mmt) cc_final: 0.7658 (mmt) REVERT: A 461 LYS cc_start: 0.8397 (tttt) cc_final: 0.8112 (tttt) REVERT: A 557 MET cc_start: 0.7890 (mmm) cc_final: 0.7413 (mmt) REVERT: A 605 LYS cc_start: 0.7758 (mttp) cc_final: 0.7363 (mtpt) REVERT: B 8 LEU cc_start: 0.9280 (pp) cc_final: 0.8838 (tp) REVERT: B 109 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8440 (tp30) REVERT: B 246 MET cc_start: 0.6993 (ptp) cc_final: 0.6403 (ptp) REVERT: B 249 ARG cc_start: 0.7087 (tpp-160) cc_final: 0.6625 (ttm170) REVERT: B 424 LEU cc_start: 0.9040 (mt) cc_final: 0.8789 (mt) REVERT: C 115 TYR cc_start: 0.2884 (t80) cc_final: 0.0796 (m-80) REVERT: E 211 MET cc_start: 0.7532 (tmm) cc_final: 0.7269 (tmm) REVERT: E 693 CYS cc_start: 0.8497 (m) cc_final: 0.7966 (m) REVERT: G 81 MET cc_start: 0.7141 (mtm) cc_final: 0.6348 (mmm) outliers start: 3 outliers final: 0 residues processed: 352 average time/residue: 0.3066 time to fit residues: 168.8762 Evaluate side-chains 291 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 115 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN F 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.159976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130491 restraints weight = 120471.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128417 restraints weight = 105253.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129591 restraints weight = 92794.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130214 restraints weight = 72451.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130315 restraints weight = 66716.594| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 1.0145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21926 Z= 0.188 Angle : 0.650 25.464 29772 Z= 0.349 Chirality : 0.039 0.174 3262 Planarity : 0.005 0.069 3750 Dihedral : 9.742 80.456 3206 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.35 % Favored : 90.53 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.56 % 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: -1.81 (0.16), residues: 2598 helix: 0.51 (0.16), residues: 1046 sheet: -1.57 (0.32), residues: 252 loop : -2.69 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 260 TYR 0.020 0.002 TYR F 497 PHE 0.020 0.002 PHE F 9 TRP 0.022 0.002 TRP E 699 HIS 0.004 0.001 HIS E 713 Details of bonding type rmsd covalent geometry : bond 0.00428 (21924) covalent geometry : angle 0.64992 (29768) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.77384 ( 4) hydrogen bonds : bond 0.05361 ( 880) hydrogen bonds : angle 5.47539 ( 2538) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 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 347 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.202 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: O 39 GLN cc_start: 0.6775 (tt0) cc_final: 0.6501 (tm-30) REVERT: A 310 CYS cc_start: 0.8386 (m) cc_final: 0.8018 (m) REVERT: A 460 MET cc_start: 0.7741 (mmt) cc_final: 0.7491 (mmt) REVERT: A 557 MET cc_start: 0.7760 (mmm) cc_final: 0.7057 (mmt) REVERT: A 605 LYS cc_start: 0.7720 (mttp) cc_final: 0.7373 (mtpt) REVERT: B 25 THR cc_start: 0.7375 (p) cc_final: 0.7130 (p) REVERT: B 109 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8245 (tp30) REVERT: B 246 MET cc_start: 0.6668 (ptp) cc_final: 0.6461 (ptp) REVERT: C 115 TYR cc_start: 0.2860 (t80) cc_final: 0.0906 (m-80) REVERT: E 211 MET cc_start: 0.7237 (tmm) cc_final: 0.7005 (tmm) REVERT: E 693 CYS cc_start: 0.8471 (m) cc_final: 0.8085 (m) REVERT: F 289 MET cc_start: 0.6670 (mmp) cc_final: 0.5950 (mmm) REVERT: F 318 PHE cc_start: 0.8412 (m-10) cc_final: 0.8136 (m-80) REVERT: F 363 LYS cc_start: 0.7348 (tttt) cc_final: 0.6569 (ptpt) REVERT: G 81 MET cc_start: 0.7188 (mtm) cc_final: 0.6403 (mmm) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.3266 time to fit residues: 176.6569 Evaluate side-chains 288 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 134 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN F 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.155550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118489 restraints weight = 117905.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119039 restraints weight = 80741.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119242 restraints weight = 63142.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120194 restraints weight = 60435.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120371 restraints weight = 51802.424| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 1.0350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21926 Z= 0.177 Angle : 0.634 25.510 29772 Z= 0.339 Chirality : 0.039 0.169 3262 Planarity : 0.005 0.077 3750 Dihedral : 9.660 79.164 3206 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.58 % Favored : 91.30 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % 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: -1.70 (0.16), residues: 2598 helix: 0.59 (0.16), residues: 1052 sheet: -1.44 (0.33), residues: 248 loop : -2.66 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 566 TYR 0.018 0.002 TYR E 305 PHE 0.036 0.002 PHE B 150 TRP 0.021 0.002 TRP E 699 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00402 (21924) covalent geometry : angle 0.63358 (29768) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.66295 ( 4) hydrogen bonds : bond 0.05248 ( 880) hydrogen bonds : angle 5.34945 ( 2538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6334.46 seconds wall clock time: 109 minutes 37.63 seconds (6577.63 seconds total)