Starting phenix.real_space_refine on Fri Feb 23 12:53:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx8_4663/02_2024/6qx8_4663.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx8_4663/02_2024/6qx8_4663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx8_4663/02_2024/6qx8_4663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx8_4663/02_2024/6qx8_4663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx8_4663/02_2024/6qx8_4663.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx8_4663/02_2024/6qx8_4663.pdb" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 134 5.16 5 C 12272 2.51 5 N 3372 2.21 5 O 3742 1.98 5 H 19050 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A ARG 582": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 583": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 563": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 614": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "C ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 424": "OE1" <-> "OE2" Residue "E ARG 490": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 580": "OE1" <-> "OE2" Residue "E ARG 582": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 583": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 599": "OE1" <-> "OE2" Residue "E GLU 610": "OE1" <-> "OE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E GLU 617": "OE1" <-> "OE2" Residue "E GLU 661": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F GLU 277": "OE1" <-> "OE2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 563": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 614": "OE1" <-> "OE2" Residue "F GLU 618": "OE1" <-> "OE2" Residue "G ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38594 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 8141 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 486} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 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: 17.22, per 1000 atoms: 0.45 Number of scatterers: 38594 At special positions: 0 Unit cell: (192.955, 103.257, 91.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 134 16.00 P 24 15.00 O 3742 8.00 N 3372 7.00 C 12272 6.00 H 19050 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.45 Conformation dependent library (CDL) restraints added in 4.2 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4492 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 16 sheets defined 48.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 4.106A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.841A pdb=" N ASP A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.746A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.048A pdb=" N CYS A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.596A pdb=" N TYR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 476 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 581 through 603 Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.251A pdb=" N GLU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.503A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 16 through 22 removed outlier: 4.513A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.690A pdb=" N VAL B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.677A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 161' Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 245 through 266 removed outlier: 3.678A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.589A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.741A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.816A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 5.417A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.833A pdb=" N SER B 422 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 521 through 536 Processing helix chain 'B' and resid 540 through 560 removed outlier: 4.077A pdb=" N MET B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.793A pdb=" N LEU B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.998A pdb=" N LEU B 611 " --> pdb=" O PRO B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.168A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.832A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.740A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 240 through 249 removed outlier: 4.106A pdb=" N GLY E 244 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.841A pdb=" N ASP E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE E 314 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 351 removed outlier: 3.746A pdb=" N TYR E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 380 through 386 removed outlier: 4.048A pdb=" N CYS E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 416 Processing helix chain 'E' and resid 433 through 452 removed outlier: 3.596A pdb=" N TYR E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 476 Processing helix chain 'E' and resid 572 through 580 Processing helix chain 'E' and resid 581 through 603 Processing helix chain 'E' and resid 608 through 613 removed outlier: 4.252A pdb=" N GLU E 613 " --> pdb=" O LYS E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 650 Processing helix chain 'E' and resid 652 through 674 removed outlier: 3.503A pdb=" N GLU E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 694 Processing helix chain 'E' and resid 697 through 715 Processing helix chain 'F' and resid 7 through 12 Processing helix chain 'F' and resid 16 through 22 removed outlier: 4.513A pdb=" N SER F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 50 Processing helix chain 'F' and resid 84 through 99 removed outlier: 3.690A pdb=" N VAL F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 117 Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 138 through 153 Processing helix chain 'F' and resid 156 through 161 removed outlier: 3.678A pdb=" N SER F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 156 through 161' Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'F' and resid 213 through 222 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.677A pdb=" N GLY F 250 " --> pdb=" O MET F 246 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE F 251 " --> pdb=" O GLN F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 291 removed outlier: 3.590A pdb=" N ALA F 283 " --> pdb=" O LYS F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 removed outlier: 3.741A pdb=" N GLN F 313 " --> pdb=" O TRP F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.816A pdb=" N PHE F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 345 removed outlier: 5.417A pdb=" N ALA F 340 " --> pdb=" O VAL F 336 " (cutoff:3.500A) Proline residue: F 341 - end of helix Processing helix chain 'F' and resid 371 through 373 No H-bonds generated for 'chain 'F' and resid 371 through 373' Processing helix chain 'F' and resid 382 through 393 Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.834A pdb=" N SER F 422 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 423 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 427 " --> pdb=" O ILE F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 473 Processing helix chain 'F' and resid 521 through 536 Processing helix chain 'F' and resid 540 through 560 removed outlier: 4.077A pdb=" N MET F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 583 removed outlier: 3.793A pdb=" N LEU F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 581 " --> pdb=" O LYS F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.997A pdb=" N LEU F 611 " --> pdb=" O PRO F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 616 No H-bonds generated for 'chain 'F' and resid 614 through 616' Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.168A pdb=" N MET G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 100 removed outlier: 3.832A pdb=" N VAL G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.740A pdb=" N TYR G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE G 119 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 125 " --> pdb=" O LYS G 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 490 removed outlier: 5.900A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 501 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 525 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 524 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 564 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 559 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.932A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 621 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.510A pdb=" N ASP B 130 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.716A pdb=" N ILE B 397 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 400 " --> pdb=" O ILE B 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 437 through 441 removed outlier: 3.620A pdb=" N TRP B 437 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 441 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.497A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 59 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 390 through 391 Processing sheet with id=AB1, first strand: chain 'E' and resid 481 through 490 removed outlier: 5.898A pdb=" N GLN E 481 " --> pdb=" O ILE E 505 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE E 505 " --> pdb=" O GLN E 481 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE E 483 " --> pdb=" O PHE E 503 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE E 503 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET E 485 " --> pdb=" O TYR E 501 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 501 " --> pdb=" O MET E 485 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR E 501 " --> pdb=" O PHE E 525 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E 525 " --> pdb=" O TYR E 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU E 524 " --> pdb=" O TYR E 564 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E 564 " --> pdb=" O GLU E 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG E 559 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU E 563 " --> pdb=" O GLU E 544 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLU E 544 " --> pdb=" O LEU E 563 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E 565 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL E 542 " --> pdb=" O VAL E 565 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 627 through 631 removed outlier: 6.933A pdb=" N GLY E 627 " --> pdb=" O GLU E 623 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU E 623 " --> pdb=" O GLY E 627 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU E 629 " --> pdb=" O ILE E 621 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 621 " --> pdb=" O GLU E 629 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 55 through 57 Processing sheet with id=AB4, first strand: chain 'F' and resid 128 through 130 removed outlier: 3.510A pdb=" N ASP F 130 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 135 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 396 through 397 removed outlier: 3.717A pdb=" N ILE F 397 " --> pdb=" O THR F 400 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 400 " --> pdb=" O ILE F 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 437 through 441 removed outlier: 3.619A pdb=" N TRP F 437 " --> pdb=" O ASN F 452 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 441 " --> pdb=" O ALA F 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 667 through 668 removed outlier: 4.347A pdb=" N ILE F 667 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 57 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 59 " --> pdb=" O VAL G 89 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.62 Time building geometry restraints manager: 32.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.47 - 0.74: 2 0.74 - 1.01: 19010 1.01 - 1.28: 3228 1.28 - 1.55: 16521 1.55 - 1.82: 305 Warning: very small bond lengths. Bond restraints: 39066 Sorted by residual: bond pdb=" N2 G H 12 " pdb=" H21 G H 12 " ideal model delta sigma weight residual 0.860 0.467 0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" N2 G D 12 " pdb=" H21 G D 12 " ideal model delta sigma weight residual 0.860 0.472 0.388 2.00e-02 2.50e+03 3.76e+02 bond pdb=" ND2 ASN F 532 " pdb="HD22 ASN F 532 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN F 532 " pdb="HD21 ASN F 532 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" NZ LYS F 531 " pdb=" HZ2 LYS F 531 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 39061 not shown) Histogram of bond angle deviations from ideal: 1.79 - 29.61: 2 29.61 - 57.43: 0 57.43 - 85.24: 4 85.24 - 113.06: 46014 113.06 - 140.88: 24538 Bond angle restraints: 70558 Sorted by residual: angle pdb=" C2 G H 12 " pdb=" N2 G H 12 " pdb=" H21 G H 12 " ideal model delta sigma weight residual 120.00 1.79 118.21 3.00e+00 1.11e-01 1.55e+03 angle pdb=" C2 G D 12 " pdb=" N2 G D 12 " pdb=" H21 G D 12 " ideal model delta sigma weight residual 120.00 4.49 115.51 3.00e+00 1.11e-01 1.48e+03 angle pdb=" CA GLY F 35 " pdb=" N GLY F 35 " pdb=" H GLY F 35 " ideal model delta sigma weight residual 114.26 58.70 55.57 3.00e+00 1.11e-01 3.43e+02 angle pdb=" C THR F 34 " pdb=" N GLY F 35 " pdb=" H GLY F 35 " ideal model delta sigma weight residual 124.56 69.21 55.35 3.00e+00 1.11e-01 3.40e+02 angle pdb=" C THR B 34 " pdb=" N GLY B 35 " pdb=" H GLY B 35 " ideal model delta sigma weight residual 124.55 74.32 50.24 3.00e+00 1.11e-01 2.80e+02 ... (remaining 70553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 15815 17.66 - 35.33: 1973 35.33 - 52.99: 458 52.99 - 70.66: 135 70.66 - 88.32: 33 Dihedral angle restraints: 18414 sinusoidal: 10292 harmonic: 8122 Sorted by residual: dihedral pdb=" CA SER A 571 " pdb=" C SER A 571 " pdb=" N LYS A 572 " pdb=" CA LYS A 572 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA SER E 571 " pdb=" C SER E 571 " pdb=" N LYS E 572 " pdb=" CA LYS E 572 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LEU E 283 " pdb=" C LEU E 283 " pdb=" N LEU E 284 " pdb=" CA LEU E 284 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 18411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2580 0.067 - 0.134: 374 0.134 - 0.201: 33 0.201 - 0.267: 3 0.267 - 0.334: 2 Chirality restraints: 2992 Sorted by residual: chirality pdb=" CA SER B 511 " pdb=" N SER B 511 " pdb=" C SER B 511 " pdb=" CB SER B 511 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA SER F 511 " pdb=" N SER F 511 " pdb=" C SER F 511 " pdb=" CB SER F 511 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA THR F 528 " pdb=" N THR F 528 " pdb=" C THR F 528 " pdb=" CB THR F 528 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2989 not shown) Planarity restraints: 5686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 514 " -0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" N SER B 515 " 0.067 2.00e-02 2.50e+03 pdb=" CA SER B 515 " -0.017 2.00e-02 2.50e+03 pdb=" H SER B 515 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 530 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C PRO E 530 " 0.066 2.00e-02 2.50e+03 pdb=" O PRO E 530 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG E 531 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 530 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C PRO A 530 " -0.066 2.00e-02 2.50e+03 pdb=" O PRO A 530 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG A 531 " 0.022 2.00e-02 2.50e+03 ... (remaining 5683 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.93: 239 1.93 - 2.60: 46957 2.60 - 3.27: 119734 3.27 - 3.93: 146384 3.93 - 4.60: 233822 Nonbonded interactions: 547136 Sorted by model distance: nonbonded pdb=" HE1 TYR F 24 " pdb=" HG3 PRO F 28 " model vdw 1.268 2.270 nonbonded pdb="HH11 ARG E 583 " pdb=" H SER F 511 " model vdw 1.508 2.100 nonbonded pdb=" H ILE F 517 " pdb=" OD2 ASP F 522 " model vdw 1.515 1.850 nonbonded pdb=" H ILE B 517 " pdb=" OD2 ASP B 522 " model vdw 1.526 1.850 nonbonded pdb="HH11 ARG A 583 " pdb=" H SER B 511 " model vdw 1.538 2.100 ... (remaining 547131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.970 Extract box with map and model: 5.040 Check model and map are aligned: 0.590 Set scattering table: 0.350 Process input model: 119.500 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 20016 Z= 0.535 Angle : 0.938 19.692 27182 Z= 0.519 Chirality : 0.047 0.334 2992 Planarity : 0.007 0.085 3412 Dihedral : 15.538 88.323 7686 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.97 % Favored : 91.86 % Rotamer: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.15), residues: 2360 helix: -1.90 (0.13), residues: 1046 sheet: -3.80 (0.32), residues: 184 loop : -2.82 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 577 HIS 0.008 0.002 HIS E 326 PHE 0.030 0.002 PHE E 520 TYR 0.018 0.002 TYR B 467 ARG 0.023 0.001 ARG E 716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 503 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 500 time to evaluate : 3.146 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: A 237 GLU cc_start: 0.7745 (pm20) cc_final: 0.7459 (mp0) REVERT: A 460 MET cc_start: 0.7212 (mmt) cc_final: 0.6786 (mtt) REVERT: A 480 PHE cc_start: 0.7655 (m-10) cc_final: 0.7444 (m-10) REVERT: A 496 ARG cc_start: 0.5921 (ptp90) cc_final: 0.5400 (ptt180) REVERT: A 650 TYR cc_start: 0.8848 (m-80) cc_final: 0.8630 (m-10) REVERT: B 70 ASP cc_start: 0.6170 (m-30) cc_final: 0.5011 (t0) REVERT: B 87 CYS cc_start: 0.8402 (m) cc_final: 0.7986 (m) REVERT: B 105 ASN cc_start: 0.9027 (m-40) cc_final: 0.8820 (m-40) REVERT: B 111 MET cc_start: 0.7048 (mmm) cc_final: 0.6841 (mmm) REVERT: B 127 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6995 (mm-40) REVERT: B 343 MET cc_start: 0.7827 (ptp) cc_final: 0.7567 (ptp) REVERT: B 348 MET cc_start: 0.6876 (ttm) cc_final: 0.5688 (pmm) REVERT: B 439 ASP cc_start: 0.7762 (t0) cc_final: 0.7552 (t0) REVERT: B 470 CYS cc_start: 0.8445 (t) cc_final: 0.8191 (t) REVERT: C 78 TRP cc_start: 0.7298 (p-90) cc_final: 0.6087 (p-90) REVERT: E 370 LEU cc_start: 0.8410 (mt) cc_final: 0.8142 (mt) REVERT: E 460 MET cc_start: 0.7200 (mmt) cc_final: 0.6858 (mtt) REVERT: E 496 ARG cc_start: 0.5867 (ptp90) cc_final: 0.5321 (ptt180) REVERT: E 661 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7185 (mm-30) REVERT: E 706 TRP cc_start: 0.7097 (m-10) cc_final: 0.6159 (m-10) REVERT: F 70 ASP cc_start: 0.6089 (m-30) cc_final: 0.4943 (t0) REVERT: F 87 CYS cc_start: 0.8463 (m) cc_final: 0.8229 (m) REVERT: F 105 ASN cc_start: 0.9053 (m-40) cc_final: 0.8792 (m-40) REVERT: F 127 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6761 (mm-40) REVERT: F 312 ASN cc_start: 0.7272 (m110) cc_final: 0.6223 (p0) REVERT: F 348 MET cc_start: 0.6560 (ttm) cc_final: 0.5611 (pmm) REVERT: F 439 ASP cc_start: 0.7839 (t0) cc_final: 0.7609 (t0) REVERT: F 554 ASP cc_start: 0.8567 (t0) cc_final: 0.8355 (t0) REVERT: G 71 ASN cc_start: 0.7926 (p0) cc_final: 0.7624 (p0) REVERT: G 78 TRP cc_start: 0.7302 (p-90) cc_final: 0.6043 (p-90) outliers start: 3 outliers final: 0 residues processed: 502 average time/residue: 0.8396 time to fit residues: 618.4250 Evaluate side-chains 394 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 186 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 GLN F 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20016 Z= 0.215 Angle : 0.653 24.399 27182 Z= 0.348 Chirality : 0.038 0.173 2992 Planarity : 0.006 0.079 3412 Dihedral : 10.442 91.175 2936 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.74 % Favored : 93.14 % Rotamer: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.16), residues: 2360 helix: -0.80 (0.14), residues: 1084 sheet: -3.39 (0.35), residues: 188 loop : -2.58 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 619 HIS 0.005 0.001 HIS A 535 PHE 0.019 0.001 PHE F 466 TYR 0.015 0.001 TYR F 467 ARG 0.005 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 458 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 LYS cc_start: 0.6881 (tptp) cc_final: 0.6651 (tptp) REVERT: A 438 ILE cc_start: 0.8102 (mp) cc_final: 0.7390 (tp) REVERT: A 460 MET cc_start: 0.7265 (mmt) cc_final: 0.6656 (mtt) REVERT: A 496 ARG cc_start: 0.6107 (ptp90) cc_final: 0.5311 (ptt180) REVERT: B 87 CYS cc_start: 0.8402 (m) cc_final: 0.7877 (m) REVERT: B 105 ASN cc_start: 0.8896 (m-40) cc_final: 0.8385 (t0) REVERT: B 111 MET cc_start: 0.6906 (mmm) cc_final: 0.6639 (mmm) REVERT: B 226 THR cc_start: 0.5441 (p) cc_final: 0.5167 (p) REVERT: B 289 MET cc_start: 0.8097 (mmm) cc_final: 0.7758 (mmm) REVERT: B 343 MET cc_start: 0.7855 (ptp) cc_final: 0.7546 (ptp) REVERT: B 348 MET cc_start: 0.6964 (ttm) cc_final: 0.5976 (pmm) REVERT: B 386 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7565 (ttm170) REVERT: B 439 ASP cc_start: 0.7780 (t0) cc_final: 0.7540 (t0) REVERT: B 470 CYS cc_start: 0.8342 (t) cc_final: 0.8090 (t) REVERT: B 514 VAL cc_start: 0.8482 (m) cc_final: 0.8022 (p) REVERT: C 60 ASP cc_start: 0.8228 (p0) cc_final: 0.8007 (p0) REVERT: E 438 ILE cc_start: 0.8206 (mp) cc_final: 0.7524 (tp) REVERT: E 460 MET cc_start: 0.7259 (mmt) cc_final: 0.6729 (mtt) REVERT: E 478 ASP cc_start: 0.7933 (p0) cc_final: 0.7728 (p0) REVERT: E 496 ARG cc_start: 0.5650 (ptp90) cc_final: 0.5256 (ptt180) REVERT: E 535 HIS cc_start: 0.5545 (p-80) cc_final: 0.5191 (p-80) REVERT: F 87 CYS cc_start: 0.8538 (m) cc_final: 0.8220 (m) REVERT: F 105 ASN cc_start: 0.8908 (m-40) cc_final: 0.8325 (t0) REVERT: F 124 GLN cc_start: 0.7569 (mp10) cc_final: 0.6802 (pp30) REVERT: F 312 ASN cc_start: 0.7239 (m110) cc_final: 0.6320 (p0) REVERT: F 386 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7600 (ttm170) REVERT: F 439 ASP cc_start: 0.7647 (t0) cc_final: 0.7373 (t0) REVERT: F 554 ASP cc_start: 0.8496 (t0) cc_final: 0.8283 (t0) REVERT: G 81 MET cc_start: 0.6278 (mpp) cc_final: 0.5955 (ptt) outliers start: 1 outliers final: 1 residues processed: 459 average time/residue: 0.7714 time to fit residues: 537.7160 Evaluate side-chains 394 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.2980 chunk 67 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20016 Z= 0.345 Angle : 0.675 24.261 27182 Z= 0.362 Chirality : 0.039 0.171 2992 Planarity : 0.006 0.064 3412 Dihedral : 10.374 86.842 2936 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.39 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.16), residues: 2360 helix: -0.56 (0.14), residues: 1084 sheet: -3.46 (0.34), residues: 192 loop : -2.44 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 619 HIS 0.007 0.001 HIS E 326 PHE 0.023 0.002 PHE E 520 TYR 0.032 0.002 TYR B 467 ARG 0.006 0.001 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8157 (mp) cc_final: 0.7482 (tp) REVERT: A 460 MET cc_start: 0.7281 (mmt) cc_final: 0.6677 (mtt) REVERT: A 496 ARG cc_start: 0.5964 (ptp90) cc_final: 0.5335 (ptt180) REVERT: A 575 MET cc_start: 0.7246 (mtp) cc_final: 0.7041 (mtp) REVERT: A 619 TRP cc_start: 0.6525 (m100) cc_final: 0.6289 (m100) REVERT: B 87 CYS cc_start: 0.8453 (m) cc_final: 0.7956 (m) REVERT: B 105 ASN cc_start: 0.8881 (m-40) cc_final: 0.8389 (t0) REVERT: B 111 MET cc_start: 0.6954 (mmm) cc_final: 0.6696 (mmm) REVERT: B 226 THR cc_start: 0.5334 (p) cc_final: 0.5016 (p) REVERT: B 289 MET cc_start: 0.8067 (mmm) cc_final: 0.7729 (mmm) REVERT: B 343 MET cc_start: 0.7925 (ptp) cc_final: 0.7599 (ptp) REVERT: B 348 MET cc_start: 0.7204 (ttm) cc_final: 0.6162 (pmm) REVERT: B 386 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7457 (tmm160) REVERT: B 438 TRP cc_start: 0.8157 (p90) cc_final: 0.7941 (p90) REVERT: B 439 ASP cc_start: 0.7846 (t0) cc_final: 0.7540 (t0) REVERT: B 470 CYS cc_start: 0.8435 (t) cc_final: 0.8167 (t) REVERT: B 514 VAL cc_start: 0.8539 (m) cc_final: 0.8200 (p) REVERT: C 60 ASP cc_start: 0.8218 (p0) cc_final: 0.7979 (p0) REVERT: E 438 ILE cc_start: 0.8332 (mp) cc_final: 0.7783 (tp) REVERT: E 460 MET cc_start: 0.7327 (mmt) cc_final: 0.6769 (mtt) REVERT: E 465 ILE cc_start: 0.8627 (mt) cc_final: 0.8342 (tt) REVERT: E 496 ARG cc_start: 0.5655 (ptp90) cc_final: 0.5259 (ptt180) REVERT: E 706 TRP cc_start: 0.7539 (m-10) cc_final: 0.6904 (m-10) REVERT: F 87 CYS cc_start: 0.8566 (m) cc_final: 0.8315 (m) REVERT: F 105 ASN cc_start: 0.8895 (m-40) cc_final: 0.8294 (t0) REVERT: F 312 ASN cc_start: 0.7538 (m110) cc_final: 0.6492 (p0) REVERT: F 348 MET cc_start: 0.6958 (ttm) cc_final: 0.5944 (pmm) REVERT: F 438 TRP cc_start: 0.8130 (p90) cc_final: 0.7842 (p90) REVERT: F 439 ASP cc_start: 0.7808 (t0) cc_final: 0.7518 (t0) REVERT: F 554 ASP cc_start: 0.8696 (t0) cc_final: 0.8493 (t0) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.7450 time to fit residues: 500.4437 Evaluate side-chains 385 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20016 Z= 0.216 Angle : 0.608 24.695 27182 Z= 0.321 Chirality : 0.038 0.173 2992 Planarity : 0.005 0.058 3412 Dihedral : 10.224 85.823 2936 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.63 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.17), residues: 2360 helix: -0.24 (0.15), residues: 1086 sheet: -3.27 (0.35), residues: 192 loop : -2.31 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 577 HIS 0.004 0.001 HIS E 326 PHE 0.018 0.001 PHE F 466 TYR 0.027 0.001 TYR B 467 ARG 0.003 0.000 ARG E 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 457 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8178 (mtpp) REVERT: A 438 ILE cc_start: 0.8118 (mp) cc_final: 0.7514 (tp) REVERT: A 460 MET cc_start: 0.7277 (mmt) cc_final: 0.6664 (mtt) REVERT: A 496 ARG cc_start: 0.5929 (ptp90) cc_final: 0.5314 (ptt180) REVERT: A 619 TRP cc_start: 0.6622 (m100) cc_final: 0.6337 (m100) REVERT: B 105 ASN cc_start: 0.8846 (m-40) cc_final: 0.8377 (t0) REVERT: B 111 MET cc_start: 0.6907 (mmm) cc_final: 0.6628 (mmm) REVERT: B 226 THR cc_start: 0.5318 (p) cc_final: 0.4959 (p) REVERT: B 343 MET cc_start: 0.7786 (ptp) cc_final: 0.7555 (ptp) REVERT: B 348 MET cc_start: 0.7205 (ttm) cc_final: 0.6155 (pmm) REVERT: B 372 MET cc_start: 0.8001 (ppp) cc_final: 0.7544 (tmm) REVERT: B 386 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7410 (tmm160) REVERT: B 438 TRP cc_start: 0.8091 (p90) cc_final: 0.7871 (p90) REVERT: B 470 CYS cc_start: 0.8316 (t) cc_final: 0.8063 (t) REVERT: B 581 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6670 (mm-30) REVERT: B 616 MET cc_start: 0.4813 (mtp) cc_final: 0.4588 (mtp) REVERT: C 60 ASP cc_start: 0.8260 (p0) cc_final: 0.8034 (p0) REVERT: E 438 ILE cc_start: 0.8320 (mp) cc_final: 0.7745 (tp) REVERT: E 460 MET cc_start: 0.7143 (mmt) cc_final: 0.6645 (mtt) REVERT: E 465 ILE cc_start: 0.8651 (mt) cc_final: 0.8327 (tt) REVERT: E 496 ARG cc_start: 0.5649 (ptp90) cc_final: 0.5168 (ptt180) REVERT: F 87 CYS cc_start: 0.8534 (m) cc_final: 0.8140 (m) REVERT: F 105 ASN cc_start: 0.8868 (m-40) cc_final: 0.8247 (t0) REVERT: F 226 THR cc_start: 0.5273 (p) cc_final: 0.4963 (p) REVERT: F 312 ASN cc_start: 0.7507 (m110) cc_final: 0.6474 (p0) REVERT: F 372 MET cc_start: 0.8039 (ppp) cc_final: 0.7740 (tmm) REVERT: F 554 ASP cc_start: 0.8670 (t0) cc_final: 0.8436 (t0) REVERT: G 110 HIS cc_start: 0.5150 (p90) cc_final: 0.4934 (p90) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.7373 time to fit residues: 513.0525 Evaluate side-chains 395 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** F 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 20016 Z= 0.342 Angle : 0.660 24.394 27182 Z= 0.352 Chirality : 0.039 0.164 2992 Planarity : 0.005 0.057 3412 Dihedral : 10.278 85.405 2936 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.81 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.17), residues: 2360 helix: -0.22 (0.15), residues: 1082 sheet: -3.27 (0.36), residues: 184 loop : -2.40 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 537 HIS 0.007 0.001 HIS E 326 PHE 0.022 0.002 PHE E 520 TYR 0.027 0.002 TYR B 467 ARG 0.004 0.000 ARG E 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 3.142 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: A 318 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8071 (mtpp) REVERT: A 438 ILE cc_start: 0.8255 (mp) cc_final: 0.7791 (mm) REVERT: A 460 MET cc_start: 0.7216 (mmt) cc_final: 0.6681 (mtt) REVERT: A 496 ARG cc_start: 0.5976 (ptp90) cc_final: 0.5286 (ptt180) REVERT: A 621 ILE cc_start: 0.7306 (pt) cc_final: 0.7081 (mp) REVERT: B 105 ASN cc_start: 0.8876 (m-40) cc_final: 0.8376 (t0) REVERT: B 111 MET cc_start: 0.6971 (mmm) cc_final: 0.6729 (mmm) REVERT: B 131 TRP cc_start: 0.7350 (p90) cc_final: 0.7003 (p90) REVERT: B 226 THR cc_start: 0.5249 (p) cc_final: 0.4973 (p) REVERT: B 343 MET cc_start: 0.7869 (ptp) cc_final: 0.7653 (ptp) REVERT: B 348 MET cc_start: 0.7220 (ttm) cc_final: 0.6181 (pmm) REVERT: B 386 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7652 (ttm170) REVERT: B 439 ASP cc_start: 0.7959 (t0) cc_final: 0.7643 (t0) REVERT: B 470 CYS cc_start: 0.8360 (t) cc_final: 0.8013 (t) REVERT: C 60 ASP cc_start: 0.8332 (p0) cc_final: 0.8091 (p0) REVERT: E 438 ILE cc_start: 0.8375 (mp) cc_final: 0.7735 (tp) REVERT: E 460 MET cc_start: 0.7209 (mmt) cc_final: 0.6753 (mtt) REVERT: E 465 ILE cc_start: 0.8662 (mt) cc_final: 0.8392 (tt) REVERT: E 496 ARG cc_start: 0.5811 (ptp90) cc_final: 0.5129 (ptt180) REVERT: E 523 MET cc_start: 0.8708 (mtt) cc_final: 0.8493 (mtt) REVERT: E 661 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7432 (mt-10) REVERT: F 87 CYS cc_start: 0.8601 (m) cc_final: 0.8170 (m) REVERT: F 105 ASN cc_start: 0.8895 (m-40) cc_final: 0.8281 (t0) REVERT: F 226 THR cc_start: 0.5257 (p) cc_final: 0.4978 (p) REVERT: F 312 ASN cc_start: 0.7740 (m110) cc_final: 0.6650 (p0) REVERT: F 348 MET cc_start: 0.7159 (ttm) cc_final: 0.5878 (pmm) REVERT: F 438 TRP cc_start: 0.8191 (p90) cc_final: 0.7873 (p90) REVERT: F 439 ASP cc_start: 0.7939 (t0) cc_final: 0.7682 (t0) REVERT: F 514 VAL cc_start: 0.8573 (m) cc_final: 0.8219 (p) REVERT: F 581 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6372 (mm-30) REVERT: G 110 HIS cc_start: 0.5281 (p90) cc_final: 0.5070 (p90) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.7385 time to fit residues: 501.7948 Evaluate side-chains 390 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN E 591 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20016 Z= 0.233 Angle : 0.613 24.775 27182 Z= 0.323 Chirality : 0.038 0.165 2992 Planarity : 0.005 0.055 3412 Dihedral : 10.162 84.910 2936 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.05 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2360 helix: 0.13 (0.15), residues: 1066 sheet: -2.89 (0.40), residues: 168 loop : -2.31 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 619 HIS 0.004 0.001 HIS E 326 PHE 0.017 0.002 PHE F 466 TYR 0.024 0.001 TYR B 467 ARG 0.003 0.000 ARG E 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 3.204 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: A 318 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8076 (mtpp) REVERT: A 438 ILE cc_start: 0.8220 (mp) cc_final: 0.7513 (tp) REVERT: A 460 MET cc_start: 0.7159 (mmt) cc_final: 0.6755 (mtt) REVERT: A 496 ARG cc_start: 0.5929 (ptp90) cc_final: 0.5233 (ptt180) REVERT: A 621 ILE cc_start: 0.7212 (pt) cc_final: 0.6994 (mp) REVERT: B 105 ASN cc_start: 0.8854 (m-40) cc_final: 0.8376 (t0) REVERT: B 111 MET cc_start: 0.6983 (mmm) cc_final: 0.6751 (mmm) REVERT: B 131 TRP cc_start: 0.7299 (p90) cc_final: 0.6913 (p90) REVERT: B 226 THR cc_start: 0.5381 (p) cc_final: 0.5031 (p) REVERT: B 348 MET cc_start: 0.7348 (ttm) cc_final: 0.6106 (pmm) REVERT: B 372 MET cc_start: 0.7903 (ppp) cc_final: 0.7347 (tmm) REVERT: B 386 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7578 (ttm170) REVERT: B 408 MET cc_start: 0.7726 (mmm) cc_final: 0.7503 (mmm) REVERT: B 439 ASP cc_start: 0.7865 (t0) cc_final: 0.7545 (t0) REVERT: B 470 CYS cc_start: 0.8314 (t) cc_final: 0.7961 (t) REVERT: C 60 ASP cc_start: 0.8318 (p0) cc_final: 0.8078 (p0) REVERT: E 438 ILE cc_start: 0.8344 (mp) cc_final: 0.7709 (tp) REVERT: E 460 MET cc_start: 0.7330 (mmt) cc_final: 0.6762 (mtt) REVERT: E 496 ARG cc_start: 0.5896 (ptp90) cc_final: 0.5079 (ptt180) REVERT: E 523 MET cc_start: 0.8667 (mtt) cc_final: 0.8461 (mtt) REVERT: E 621 ILE cc_start: 0.7264 (pt) cc_final: 0.7030 (mt) REVERT: E 661 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7397 (mt-10) REVERT: F 87 CYS cc_start: 0.8512 (m) cc_final: 0.8085 (m) REVERT: F 105 ASN cc_start: 0.8866 (m-40) cc_final: 0.8280 (t0) REVERT: F 226 THR cc_start: 0.5319 (p) cc_final: 0.5035 (p) REVERT: F 312 ASN cc_start: 0.7632 (m110) cc_final: 0.6616 (p0) REVERT: F 348 MET cc_start: 0.7321 (ttm) cc_final: 0.5930 (pmm) REVERT: F 372 MET cc_start: 0.7942 (ppp) cc_final: 0.7521 (tmm) REVERT: F 438 TRP cc_start: 0.8010 (p90) cc_final: 0.7789 (p90) REVERT: F 439 ASP cc_start: 0.7946 (t0) cc_final: 0.7711 (t0) REVERT: F 491 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7408 (tt0) REVERT: F 581 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6366 (mm-30) REVERT: G 110 HIS cc_start: 0.5332 (p90) cc_final: 0.5127 (p90) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.7035 time to fit residues: 489.8965 Evaluate side-chains 399 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 ASN E 590 GLN E 591 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 20016 Z= 0.289 Angle : 0.631 24.870 27182 Z= 0.335 Chirality : 0.038 0.163 2992 Planarity : 0.005 0.053 3412 Dihedral : 10.175 85.081 2936 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.07 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2360 helix: 0.16 (0.15), residues: 1058 sheet: -3.05 (0.40), residues: 168 loop : -2.31 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 619 HIS 0.006 0.001 HIS E 326 PHE 0.019 0.002 PHE E 520 TYR 0.027 0.001 TYR B 467 ARG 0.004 0.000 ARG E 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 438 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8167 (mp) cc_final: 0.7465 (tp) REVERT: A 460 MET cc_start: 0.7147 (mmt) cc_final: 0.6745 (mtt) REVERT: A 496 ARG cc_start: 0.5914 (ptp90) cc_final: 0.5256 (ptt180) REVERT: A 575 MET cc_start: 0.7188 (mtp) cc_final: 0.6943 (mtp) REVERT: A 621 ILE cc_start: 0.7183 (pt) cc_final: 0.6934 (mp) REVERT: B 105 ASN cc_start: 0.8838 (m-40) cc_final: 0.8362 (t0) REVERT: B 226 THR cc_start: 0.5391 (p) cc_final: 0.5107 (p) REVERT: B 348 MET cc_start: 0.7365 (ttm) cc_final: 0.6125 (pmm) REVERT: B 372 MET cc_start: 0.7925 (ppp) cc_final: 0.7534 (tmm) REVERT: B 386 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7581 (ttm170) REVERT: B 439 ASP cc_start: 0.7935 (t0) cc_final: 0.7661 (t0) REVERT: B 470 CYS cc_start: 0.8314 (t) cc_final: 0.7945 (t) REVERT: C 60 ASP cc_start: 0.8352 (p0) cc_final: 0.8109 (p0) REVERT: E 438 ILE cc_start: 0.8339 (mp) cc_final: 0.7672 (tp) REVERT: E 460 MET cc_start: 0.7326 (mmt) cc_final: 0.6830 (mtt) REVERT: E 496 ARG cc_start: 0.6000 (ptp90) cc_final: 0.5154 (ptt180) REVERT: E 621 ILE cc_start: 0.7181 (pt) cc_final: 0.6954 (mt) REVERT: E 661 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7366 (mt-10) REVERT: F 87 CYS cc_start: 0.8574 (m) cc_final: 0.8121 (m) REVERT: F 105 ASN cc_start: 0.8843 (m-40) cc_final: 0.8266 (t0) REVERT: F 226 THR cc_start: 0.5270 (p) cc_final: 0.4990 (p) REVERT: F 312 ASN cc_start: 0.7798 (m110) cc_final: 0.6794 (p0) REVERT: F 348 MET cc_start: 0.7321 (ttm) cc_final: 0.5911 (pmm) REVERT: F 372 MET cc_start: 0.7964 (ppp) cc_final: 0.7590 (tmm) REVERT: F 438 TRP cc_start: 0.8151 (p90) cc_final: 0.7917 (p90) REVERT: F 439 ASP cc_start: 0.7972 (t0) cc_final: 0.7738 (t0) REVERT: G 110 HIS cc_start: 0.5366 (p90) cc_final: 0.5154 (p90) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.7096 time to fit residues: 476.0867 Evaluate side-chains 397 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20016 Z= 0.206 Angle : 0.601 25.025 27182 Z= 0.315 Chirality : 0.037 0.166 2992 Planarity : 0.005 0.084 3412 Dihedral : 10.076 87.105 2936 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.31 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.17), residues: 2360 helix: 0.36 (0.16), residues: 1058 sheet: -2.89 (0.40), residues: 168 loop : -2.20 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 537 HIS 0.004 0.001 HIS E 326 PHE 0.017 0.001 PHE F 466 TYR 0.025 0.001 TYR B 467 ARG 0.008 0.000 ARG F 623 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8173 (mp) cc_final: 0.7476 (tp) REVERT: A 460 MET cc_start: 0.7127 (mmt) cc_final: 0.6722 (mtt) REVERT: A 496 ARG cc_start: 0.5980 (ptp90) cc_final: 0.5210 (ptt180) REVERT: A 621 ILE cc_start: 0.7122 (pt) cc_final: 0.6856 (mt) REVERT: A 661 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6765 (mm-30) REVERT: B 105 ASN cc_start: 0.8869 (m-40) cc_final: 0.8354 (t0) REVERT: B 226 THR cc_start: 0.5403 (p) cc_final: 0.5078 (p) REVERT: B 306 ASN cc_start: 0.7940 (m110) cc_final: 0.7379 (m-40) REVERT: B 348 MET cc_start: 0.7389 (ttm) cc_final: 0.6137 (pmm) REVERT: B 372 MET cc_start: 0.8107 (ppp) cc_final: 0.7554 (tmm) REVERT: B 386 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7547 (ttm170) REVERT: B 408 MET cc_start: 0.7686 (mmm) cc_final: 0.7459 (mmm) REVERT: B 439 ASP cc_start: 0.7879 (t0) cc_final: 0.7580 (t0) REVERT: B 470 CYS cc_start: 0.8271 (t) cc_final: 0.7932 (t) REVERT: B 491 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7435 (tt0) REVERT: C 60 ASP cc_start: 0.8329 (p0) cc_final: 0.8090 (p0) REVERT: E 313 THR cc_start: 0.8106 (m) cc_final: 0.7865 (m) REVERT: E 358 LYS cc_start: 0.6967 (tptp) cc_final: 0.6619 (tptm) REVERT: E 438 ILE cc_start: 0.8310 (mp) cc_final: 0.7693 (tp) REVERT: E 460 MET cc_start: 0.7257 (mmt) cc_final: 0.6765 (mtt) REVERT: E 496 ARG cc_start: 0.6030 (ptp90) cc_final: 0.5184 (ptt180) REVERT: E 575 MET cc_start: 0.7067 (mtp) cc_final: 0.6823 (mtp) REVERT: E 621 ILE cc_start: 0.7153 (pt) cc_final: 0.6934 (mt) REVERT: E 661 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7369 (mt-10) REVERT: F 87 CYS cc_start: 0.8534 (m) cc_final: 0.8081 (m) REVERT: F 105 ASN cc_start: 0.8827 (m-40) cc_final: 0.8270 (t0) REVERT: F 226 THR cc_start: 0.5228 (p) cc_final: 0.4937 (p) REVERT: F 312 ASN cc_start: 0.7762 (m110) cc_final: 0.6758 (p0) REVERT: F 348 MET cc_start: 0.7307 (ttm) cc_final: 0.5894 (pmm) REVERT: F 372 MET cc_start: 0.8079 (ppp) cc_final: 0.7659 (tmm) REVERT: F 438 TRP cc_start: 0.8020 (p90) cc_final: 0.7742 (p90) REVERT: F 491 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7488 (tt0) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.7114 time to fit residues: 498.6144 Evaluate side-chains 395 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 3.9990 chunk 219 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 167 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20016 Z= 0.207 Angle : 0.599 25.088 27182 Z= 0.314 Chirality : 0.037 0.165 2992 Planarity : 0.005 0.089 3412 Dihedral : 10.001 87.618 2936 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.22 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2360 helix: 0.47 (0.16), residues: 1058 sheet: -2.86 (0.40), residues: 168 loop : -2.17 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 537 HIS 0.004 0.001 HIS F 664 PHE 0.018 0.001 PHE A 562 TYR 0.025 0.001 TYR A 445 ARG 0.012 0.000 ARG F 623 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8189 (mp) cc_final: 0.7532 (tp) REVERT: A 460 MET cc_start: 0.7164 (mmt) cc_final: 0.6764 (mtt) REVERT: A 496 ARG cc_start: 0.6017 (ptp90) cc_final: 0.5192 (ptt180) REVERT: A 621 ILE cc_start: 0.7085 (pt) cc_final: 0.6816 (mt) REVERT: A 661 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6865 (mm-30) REVERT: B 105 ASN cc_start: 0.8822 (m-40) cc_final: 0.8253 (t0) REVERT: B 226 THR cc_start: 0.5472 (p) cc_final: 0.5120 (p) REVERT: B 306 ASN cc_start: 0.7837 (m110) cc_final: 0.7228 (m-40) REVERT: B 372 MET cc_start: 0.8064 (ppp) cc_final: 0.7561 (tmm) REVERT: B 386 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7545 (ttm170) REVERT: B 403 LEU cc_start: 0.6629 (pt) cc_final: 0.6397 (pt) REVERT: B 439 ASP cc_start: 0.7871 (t0) cc_final: 0.7597 (t0) REVERT: B 470 CYS cc_start: 0.8297 (t) cc_final: 0.7995 (t) REVERT: B 491 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7457 (tt0) REVERT: C 60 ASP cc_start: 0.8298 (p0) cc_final: 0.8078 (p0) REVERT: E 313 THR cc_start: 0.8118 (m) cc_final: 0.7870 (m) REVERT: E 438 ILE cc_start: 0.8332 (mp) cc_final: 0.7675 (tp) REVERT: E 460 MET cc_start: 0.7319 (mmt) cc_final: 0.6751 (mtt) REVERT: E 496 ARG cc_start: 0.6034 (ptp90) cc_final: 0.5219 (ptt180) REVERT: E 535 HIS cc_start: 0.5590 (p-80) cc_final: 0.5276 (p-80) REVERT: E 575 MET cc_start: 0.7049 (mtp) cc_final: 0.6770 (mtp) REVERT: E 621 ILE cc_start: 0.6991 (pt) cc_final: 0.6743 (mt) REVERT: E 661 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7342 (mt-10) REVERT: F 87 CYS cc_start: 0.8543 (m) cc_final: 0.8087 (m) REVERT: F 105 ASN cc_start: 0.8805 (m-40) cc_final: 0.8277 (t0) REVERT: F 226 THR cc_start: 0.5475 (p) cc_final: 0.5190 (p) REVERT: F 312 ASN cc_start: 0.7698 (m110) cc_final: 0.6665 (p0) REVERT: F 348 MET cc_start: 0.7254 (ttm) cc_final: 0.5822 (pmm) REVERT: F 372 MET cc_start: 0.8049 (ppp) cc_final: 0.7664 (tmm) REVERT: F 438 TRP cc_start: 0.8029 (p90) cc_final: 0.7751 (p90) REVERT: F 439 ASP cc_start: 0.7926 (t0) cc_final: 0.7721 (t0) REVERT: F 491 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7486 (tt0) REVERT: F 545 GLN cc_start: 0.7709 (mt0) cc_final: 0.7433 (mt0) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.7117 time to fit residues: 489.6999 Evaluate side-chains 401 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20016 Z= 0.192 Angle : 0.597 25.168 27182 Z= 0.312 Chirality : 0.037 0.164 2992 Planarity : 0.005 0.078 3412 Dihedral : 9.941 88.271 2936 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.14 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.18), residues: 2360 helix: 0.56 (0.16), residues: 1058 sheet: -3.20 (0.42), residues: 148 loop : -2.06 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 619 HIS 0.004 0.001 HIS F 664 PHE 0.015 0.001 PHE F 466 TYR 0.021 0.001 TYR B 467 ARG 0.013 0.000 ARG F 623 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 452 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8177 (mp) cc_final: 0.7464 (tp) REVERT: A 441 MET cc_start: 0.6241 (ptm) cc_final: 0.5957 (ptm) REVERT: A 460 MET cc_start: 0.7162 (mmt) cc_final: 0.6721 (mtt) REVERT: A 496 ARG cc_start: 0.5993 (ptp90) cc_final: 0.5279 (ptt180) REVERT: A 523 MET cc_start: 0.8637 (mtt) cc_final: 0.8429 (mtt) REVERT: A 621 ILE cc_start: 0.7074 (pt) cc_final: 0.6764 (mt) REVERT: A 661 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6806 (mm-30) REVERT: B 105 ASN cc_start: 0.8771 (m-40) cc_final: 0.8379 (t0) REVERT: B 226 THR cc_start: 0.5410 (p) cc_final: 0.5066 (p) REVERT: B 386 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7510 (ttm170) REVERT: B 403 LEU cc_start: 0.6604 (pt) cc_final: 0.6341 (pt) REVERT: B 439 ASP cc_start: 0.7838 (t0) cc_final: 0.7520 (t70) REVERT: B 470 CYS cc_start: 0.8310 (t) cc_final: 0.8012 (t) REVERT: B 491 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7402 (tt0) REVERT: C 60 ASP cc_start: 0.8313 (p0) cc_final: 0.8082 (p0) REVERT: E 313 THR cc_start: 0.8086 (m) cc_final: 0.7841 (m) REVERT: E 438 ILE cc_start: 0.8336 (mp) cc_final: 0.7628 (tp) REVERT: E 460 MET cc_start: 0.7346 (mmt) cc_final: 0.6845 (mtt) REVERT: E 496 ARG cc_start: 0.6020 (ptp90) cc_final: 0.5227 (ptt180) REVERT: E 535 HIS cc_start: 0.5667 (p-80) cc_final: 0.5226 (p90) REVERT: E 575 MET cc_start: 0.6932 (mtp) cc_final: 0.6657 (mtp) REVERT: E 621 ILE cc_start: 0.6934 (pt) cc_final: 0.6709 (mt) REVERT: E 661 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7431 (mt-10) REVERT: F 87 CYS cc_start: 0.8556 (m) cc_final: 0.8047 (m) REVERT: F 105 ASN cc_start: 0.8787 (m-40) cc_final: 0.8212 (t0) REVERT: F 124 GLN cc_start: 0.7501 (mp10) cc_final: 0.7259 (pp30) REVERT: F 226 THR cc_start: 0.5385 (p) cc_final: 0.5142 (p) REVERT: F 306 ASN cc_start: 0.7690 (m110) cc_final: 0.7042 (m-40) REVERT: F 312 ASN cc_start: 0.7604 (m110) cc_final: 0.6661 (p0) REVERT: F 348 MET cc_start: 0.7246 (ttm) cc_final: 0.5809 (pmm) REVERT: F 372 MET cc_start: 0.8038 (ppp) cc_final: 0.7690 (tmm) REVERT: F 438 TRP cc_start: 0.8056 (p90) cc_final: 0.7764 (p90) REVERT: F 439 ASP cc_start: 0.7921 (t0) cc_final: 0.7716 (t70) REVERT: F 491 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7442 (tt0) REVERT: F 545 GLN cc_start: 0.7641 (mt0) cc_final: 0.7419 (mt0) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.6963 time to fit residues: 484.0773 Evaluate side-chains 401 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.166527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140154 restraints weight = 103587.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145441 restraints weight = 51547.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148859 restraints weight = 31872.484| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20016 Z= 0.207 Angle : 0.597 25.125 27182 Z= 0.312 Chirality : 0.037 0.167 2992 Planarity : 0.005 0.073 3412 Dihedral : 9.923 88.098 2936 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.47 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 2360 helix: 0.63 (0.16), residues: 1052 sheet: -2.66 (0.42), residues: 168 loop : -2.06 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 619 HIS 0.004 0.001 HIS E 326 PHE 0.038 0.002 PHE A 562 TYR 0.023 0.001 TYR B 467 ARG 0.014 0.000 ARG E 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9452.95 seconds wall clock time: 168 minutes 22.30 seconds (10102.30 seconds total)