Starting phenix.real_space_refine on Sun Mar 24 06:31:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxe_4666/03_2024/6qxe_4666.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxe_4666/03_2024/6qxe_4666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxe_4666/03_2024/6qxe_4666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxe_4666/03_2024/6qxe_4666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxe_4666/03_2024/6qxe_4666.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxe_4666/03_2024/6qxe_4666.pdb" } resolution = 4.15 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 146 5.16 5 C 13434 2.51 5 N 3700 2.21 5 O 4106 1.98 5 H 19050 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ARG 82": "NH1" <-> "NH2" Residue "O ARG 82": "NH1" <-> "NH2" 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40460 Number of models: 1 Model: "" Number of chains: 10 Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "O" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "A" Number of atoms: 8141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 8141 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 486} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'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: 16.65, per 1000 atoms: 0.41 Number of scatterers: 40460 At special positions: 0 Unit cell: (186.84, 113.4, 102.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 146 16.00 P 24 15.00 O 4106 8.00 N 3700 7.00 C 13434 6.00 H 19050 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 30.06 Conformation dependent library (CDL) restraints added in 4.8 seconds 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4916 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 20 sheets defined 45.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.706A pdb=" N ASN M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.690A pdb=" N ASN O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.645A pdb=" N SER O 91 " --> pdb=" O PRO O 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 4.106A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.841A pdb=" N ASP A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.746A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.049A pdb=" N CYS A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.596A pdb=" N TYR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 476 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 581 through 603 Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.251A pdb=" N GLU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.503A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 16 through 22 removed outlier: 4.512A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.689A pdb=" N VAL B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.677A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 161' Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 245 through 266 removed outlier: 3.678A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.589A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.741A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.816A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 5.417A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.834A pdb=" N SER B 422 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 521 through 536 Processing helix chain 'B' and resid 540 through 560 removed outlier: 4.077A pdb=" N MET B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.793A pdb=" N LEU B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.998A pdb=" N LEU B 611 " --> pdb=" O PRO B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.168A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.832A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.741A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 240 through 249 removed outlier: 4.105A pdb=" N GLY E 244 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.841A pdb=" N ASP E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE E 314 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 351 removed outlier: 3.747A pdb=" N TYR E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 380 through 386 removed outlier: 4.047A pdb=" N CYS E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 416 Processing helix chain 'E' and resid 433 through 452 removed outlier: 3.596A pdb=" N TYR E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 476 Processing helix chain 'E' and resid 572 through 580 Processing helix chain 'E' and resid 581 through 603 Processing helix chain 'E' and resid 608 through 613 removed outlier: 4.252A pdb=" N GLU E 613 " --> pdb=" O LYS E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 650 Processing helix chain 'E' and resid 652 through 674 removed outlier: 3.503A pdb=" N GLU E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 694 Processing helix chain 'E' and resid 697 through 715 Processing helix chain 'F' and resid 7 through 12 Processing helix chain 'F' and resid 16 through 22 removed outlier: 4.513A pdb=" N SER F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 50 Processing helix chain 'F' and resid 84 through 99 removed outlier: 3.689A pdb=" N VAL F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 117 Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 138 through 153 Processing helix chain 'F' and resid 156 through 161 removed outlier: 3.678A pdb=" N SER F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 156 through 161' Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'F' and resid 213 through 222 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.678A pdb=" N GLY F 250 " --> pdb=" O MET F 246 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE F 251 " --> pdb=" O GLN F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 291 removed outlier: 3.590A pdb=" N ALA F 283 " --> pdb=" O LYS F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 removed outlier: 3.742A pdb=" N GLN F 313 " --> pdb=" O TRP F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.817A pdb=" N PHE F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 345 removed outlier: 5.417A pdb=" N ALA F 340 " --> pdb=" O VAL F 336 " (cutoff:3.500A) Proline residue: F 341 - end of helix Processing helix chain 'F' and resid 371 through 373 No H-bonds generated for 'chain 'F' and resid 371 through 373' Processing helix chain 'F' and resid 382 through 393 Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.834A pdb=" N SER F 422 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE F 423 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 427 " --> pdb=" O ILE F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 473 Processing helix chain 'F' and resid 521 through 536 Processing helix chain 'F' and resid 540 through 560 removed outlier: 4.077A pdb=" N MET F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 583 removed outlier: 3.794A pdb=" N LEU F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 581 " --> pdb=" O LYS F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.998A pdb=" N LEU F 611 " --> pdb=" O PRO F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 616 No H-bonds generated for 'chain 'F' and resid 614 through 616' Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.168A pdb=" N MET G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 100 removed outlier: 3.832A pdb=" N VAL G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.740A pdb=" N TYR G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE G 119 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU G 125 " --> pdb=" O LYS G 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.412A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET M 34 " --> pdb=" O MET M 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.522A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET O 34 " --> pdb=" O MET O 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA6, first strand: chain 'A' and resid 481 through 490 removed outlier: 5.900A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 501 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 525 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 524 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 564 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 559 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.932A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 621 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.510A pdb=" N ASP B 130 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.717A pdb=" N ILE B 397 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 400 " --> pdb=" O ILE B 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 441 removed outlier: 3.619A pdb=" N TRP B 437 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 441 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.497A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 59 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 390 through 391 Processing sheet with id=AB5, first strand: chain 'E' and resid 481 through 490 removed outlier: 5.898A pdb=" N GLN E 481 " --> pdb=" O ILE E 505 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE E 505 " --> pdb=" O GLN E 481 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE E 483 " --> pdb=" O PHE E 503 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE E 503 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET E 485 " --> pdb=" O TYR E 501 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 501 " --> pdb=" O MET E 485 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR E 501 " --> pdb=" O PHE E 525 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 525 " --> pdb=" O TYR E 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU E 524 " --> pdb=" O TYR E 564 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E 564 " --> pdb=" O GLU E 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG E 559 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU E 563 " --> pdb=" O GLU E 544 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU E 544 " --> pdb=" O LEU E 563 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL E 565 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL E 542 " --> pdb=" O VAL E 565 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 627 through 631 removed outlier: 6.933A pdb=" N GLY E 627 " --> pdb=" O GLU E 623 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU E 623 " --> pdb=" O GLY E 627 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU E 629 " --> pdb=" O ILE E 621 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 621 " --> pdb=" O GLU E 629 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 55 through 57 Processing sheet with id=AB8, first strand: chain 'F' and resid 128 through 130 removed outlier: 3.511A pdb=" N ASP F 130 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 135 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 396 through 397 removed outlier: 3.717A pdb=" N ILE F 397 " --> pdb=" O THR F 400 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 400 " --> pdb=" O ILE F 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 437 through 441 removed outlier: 3.619A pdb=" N TRP F 437 " --> pdb=" O ASN F 452 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 441 " --> pdb=" O ALA F 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 667 through 668 removed outlier: 4.347A pdb=" N ILE F 667 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 57 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 59 " --> pdb=" O VAL G 89 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.36 Time building geometry restraints manager: 31.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.47 - 0.74: 2 0.74 - 1.01: 19010 1.01 - 1.28: 3534 1.28 - 1.55: 18102 1.55 - 1.82: 326 Warning: very small bond lengths. Bond restraints: 40974 Sorted by residual: bond pdb=" N2 G H 12 " pdb=" H21 G H 12 " ideal model delta sigma weight residual 0.860 0.468 0.392 2.00e-02 2.50e+03 3.85e+02 bond pdb=" N2 G D 12 " pdb=" H21 G D 12 " ideal model delta sigma weight residual 0.860 0.473 0.387 2.00e-02 2.50e+03 3.75e+02 bond pdb=" ND2 ASN F 532 " pdb="HD22 ASN F 532 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN F 532 " pdb="HD21 ASN F 532 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" NZ LYS F 531 " pdb=" HZ3 LYS F 531 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 40969 not shown) Histogram of bond angle deviations from ideal: 1.72 - 29.54: 2 29.54 - 57.36: 0 57.36 - 85.19: 4 85.19 - 113.01: 46940 113.01 - 140.83: 26198 Bond angle restraints: 73144 Sorted by residual: angle pdb=" C2 G H 12 " pdb=" N2 G H 12 " pdb=" H21 G H 12 " ideal model delta sigma weight residual 120.00 1.72 118.28 3.00e+00 1.11e-01 1.55e+03 angle pdb=" C2 G D 12 " pdb=" N2 G D 12 " pdb=" H21 G D 12 " ideal model delta sigma weight residual 120.00 4.43 115.57 3.00e+00 1.11e-01 1.48e+03 angle pdb=" CA GLY F 35 " pdb=" N GLY F 35 " pdb=" H GLY F 35 " ideal model delta sigma weight residual 114.26 58.66 55.61 3.00e+00 1.11e-01 3.44e+02 angle pdb=" C THR F 34 " pdb=" N GLY F 35 " pdb=" H GLY F 35 " ideal model delta sigma weight residual 124.56 69.24 55.33 3.00e+00 1.11e-01 3.40e+02 angle pdb=" C THR B 34 " pdb=" N GLY B 35 " pdb=" H GLY B 35 " ideal model delta sigma weight residual 124.55 74.28 50.27 3.00e+00 1.11e-01 2.81e+02 ... (remaining 73139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 16829 17.66 - 35.33: 2059 35.33 - 52.99: 474 52.99 - 70.66: 137 70.66 - 88.32: 33 Dihedral angle restraints: 19532 sinusoidal: 10730 harmonic: 8802 Sorted by residual: dihedral pdb=" CA SER A 571 " pdb=" C SER A 571 " pdb=" N LYS A 572 " pdb=" CA LYS A 572 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA SER E 571 " pdb=" C SER E 571 " pdb=" N LYS E 572 " pdb=" CA LYS E 572 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LEU A 283 " pdb=" C LEU A 283 " pdb=" N LEU A 284 " pdb=" CA LEU A 284 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 19529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2823 0.067 - 0.134: 398 0.134 - 0.200: 36 0.200 - 0.267: 3 0.267 - 0.334: 2 Chirality restraints: 3262 Sorted by residual: chirality pdb=" CA SER B 511 " pdb=" N SER B 511 " pdb=" C SER B 511 " pdb=" CB SER B 511 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA SER F 511 " pdb=" N SER F 511 " pdb=" C SER F 511 " pdb=" CB SER F 511 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA THR F 528 " pdb=" N THR F 528 " pdb=" C THR F 528 " pdb=" CB THR F 528 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3259 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 514 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" N SER B 515 " 0.066 2.00e-02 2.50e+03 pdb=" CA SER B 515 " -0.017 2.00e-02 2.50e+03 pdb=" H SER B 515 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 530 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.46e+01 pdb=" C PRO E 530 " 0.066 2.00e-02 2.50e+03 pdb=" O PRO E 530 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG E 531 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 530 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C PRO A 530 " -0.066 2.00e-02 2.50e+03 pdb=" O PRO A 530 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG A 531 " 0.022 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.55: 11 1.55 - 2.31: 11174 2.31 - 3.07: 121080 3.07 - 3.84: 161295 3.84 - 4.60: 265198 Warning: very small nonbonded interaction distances. Nonbonded interactions: 558758 Sorted by model distance: nonbonded pdb=" CD LYS M 43 " pdb="HG13 ILE A 554 " model vdw 0.787 2.920 nonbonded pdb=" HE1 TYR F 24 " pdb=" HG3 PRO F 28 " model vdw 1.268 2.270 nonbonded pdb=" CH2 TRP O 105 " pdb="HH22 ARG B 563 " model vdw 1.277 2.800 nonbonded pdb=" O ALA M 56 " pdb=" HB3 GLU E 427 " model vdw 1.334 2.620 nonbonded pdb=" CH2 TRP M 105 " pdb="HH22 ARG F 563 " model vdw 1.392 2.800 ... (remaining 558753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.600 Extract box with map and model: 5.140 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 116.650 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 21924 Z= 0.512 Angle : 0.917 19.639 29768 Z= 0.508 Chirality : 0.047 0.334 3262 Planarity : 0.007 0.085 3750 Dihedral : 15.347 88.320 8374 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.54 % Favored : 92.30 % Rotamer: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.74 (0.14), residues: 2598 helix: -1.90 (0.13), residues: 1046 sheet: -3.03 (0.27), residues: 274 loop : -2.86 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 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) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 704 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 701 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 30 SER cc_start: 0.8624 (t) cc_final: 0.8364 (p) REVERT: M 31 ASN cc_start: 0.7393 (m-40) cc_final: 0.6725 (m-40) REVERT: A 356 ARG cc_start: 0.6616 (mtt180) cc_final: 0.6280 (mtt90) REVERT: A 450 VAL cc_start: 0.7605 (t) cc_final: 0.7302 (p) REVERT: A 557 MET cc_start: 0.6955 (mmp) cc_final: 0.6113 (mmt) REVERT: B 246 MET cc_start: 0.4954 (ptm) cc_final: 0.4487 (tpp) REVERT: B 324 TYR cc_start: 0.6959 (t80) cc_final: 0.6081 (t80) REVERT: B 501 PHE cc_start: 0.5904 (t80) cc_final: 0.5504 (t80) REVERT: B 576 LEU cc_start: 0.7250 (mt) cc_final: 0.7034 (mt) REVERT: E 431 ASP cc_start: 0.7626 (p0) cc_final: 0.7394 (p0) REVERT: E 568 ASN cc_start: 0.6682 (t0) cc_final: 0.6194 (m-40) REVERT: E 667 LEU cc_start: 0.7330 (tp) cc_final: 0.6983 (tt) REVERT: F 432 THR cc_start: 0.6553 (t) cc_final: 0.6111 (m) REVERT: F 483 TYR cc_start: 0.5400 (p90) cc_final: 0.4661 (p90) REVERT: G 81 MET cc_start: 0.6460 (mtm) cc_final: 0.5228 (mmp) outliers start: 3 outliers final: 0 residues processed: 704 average time/residue: 0.8310 time to fit residues: 864.8225 Evaluate side-chains 427 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 31 ASN O 31 ASN ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN B 313 GLN B 664 HIS E 383 ASN E 513 ASN E 675 ASN F 306 ASN F 428 GLN F 485 ASN F 533 ASN F 621 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 21924 Z= 0.317 Angle : 0.724 24.576 29768 Z= 0.388 Chirality : 0.041 0.164 3262 Planarity : 0.006 0.076 3750 Dihedral : 10.133 93.351 3206 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.97 % Favored : 91.92 % Rotamer: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % 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: -2.76 (0.15), residues: 2598 helix: -0.79 (0.14), residues: 1082 sheet: -2.57 (0.28), residues: 284 loop : -2.62 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP O 105 HIS 0.014 0.002 HIS A 510 PHE 0.038 0.002 PHE B 166 TYR 0.023 0.002 TYR M 114 ARG 0.014 0.001 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 504 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 MET cc_start: 0.6845 (mtm) cc_final: 0.6598 (mtt) REVERT: O 57 ASP cc_start: 0.6428 (t0) cc_final: 0.5994 (t70) REVERT: O 73 ASP cc_start: 0.6280 (t0) cc_final: 0.5484 (m-30) REVERT: O 83 MET cc_start: 0.7736 (mtp) cc_final: 0.7533 (mtm) REVERT: A 327 GLU cc_start: 0.6386 (tm-30) cc_final: 0.6016 (tp30) REVERT: A 363 THR cc_start: 0.8408 (t) cc_final: 0.8198 (t) REVERT: A 396 ASP cc_start: 0.5307 (t0) cc_final: 0.4886 (m-30) REVERT: A 470 LEU cc_start: 0.8851 (tp) cc_final: 0.8650 (tp) REVERT: A 521 VAL cc_start: 0.7824 (t) cc_final: 0.7413 (t) REVERT: B 109 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7887 (tp30) REVERT: B 246 MET cc_start: 0.5358 (ptm) cc_final: 0.4926 (tpp) REVERT: B 501 PHE cc_start: 0.6415 (t80) cc_final: 0.5992 (t80) REVERT: E 230 ARG cc_start: 0.6765 (mtt180) cc_final: 0.6441 (mmm-85) REVERT: F 122 LEU cc_start: 0.7763 (pp) cc_final: 0.7520 (tt) REVERT: F 616 MET cc_start: 0.7298 (mtp) cc_final: 0.7008 (mtp) REVERT: G 81 MET cc_start: 0.6311 (mtm) cc_final: 0.5642 (mmp) outliers start: 1 outliers final: 1 residues processed: 505 average time/residue: 0.7390 time to fit residues: 569.2425 Evaluate side-chains 404 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 403 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 499 ASN A 591 GLN B 16 ASN B 276 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 HIS E 499 ASN F 16 ASN F 65 GLN F 99 HIS ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN F 485 ASN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 21924 Z= 0.476 Angle : 0.849 27.623 29768 Z= 0.454 Chirality : 0.045 0.309 3262 Planarity : 0.007 0.145 3750 Dihedral : 10.194 95.680 3206 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.01 % Favored : 89.80 % Rotamer: Outliers : 0.39 % Allowed : 5.69 % Favored : 93.92 % 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: -2.86 (0.15), residues: 2598 helix: -0.69 (0.15), residues: 1054 sheet: -2.56 (0.29), residues: 260 loop : -2.86 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 332 HIS 0.011 0.002 HIS E 326 PHE 0.042 0.003 PHE C 119 TYR 0.028 0.003 TYR B 599 ARG 0.011 0.001 ARG F 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 478 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 GLN cc_start: 0.8844 (pp30) cc_final: 0.8632 (pp30) REVERT: A 557 MET cc_start: 0.8068 (mmm) cc_final: 0.7737 (mmp) REVERT: B 246 MET cc_start: 0.6003 (ptm) cc_final: 0.5159 (mmt) REVERT: B 321 MET cc_start: 0.6517 (mtp) cc_final: 0.6247 (mtp) REVERT: B 324 TYR cc_start: 0.7006 (t80) cc_final: 0.6730 (t80) REVERT: B 348 MET cc_start: 0.4897 (pmm) cc_final: 0.3581 (pmm) REVERT: B 501 PHE cc_start: 0.7100 (t80) cc_final: 0.6746 (t80) REVERT: C 57 ILE cc_start: 0.7277 (mt) cc_final: 0.6984 (mt) REVERT: C 120 GLU cc_start: 0.5160 (mt-10) cc_final: 0.4707 (tm-30) REVERT: E 401 ARG cc_start: 0.7014 (mmt180) cc_final: 0.6758 (mmt-90) REVERT: E 523 MET cc_start: 0.8563 (mtt) cc_final: 0.8268 (mtt) REVERT: E 597 GLU cc_start: 0.7122 (tt0) cc_final: 0.6877 (tt0) REVERT: F 122 LEU cc_start: 0.7941 (pp) cc_final: 0.7579 (tt) REVERT: F 362 MET cc_start: 0.6885 (ppp) cc_final: 0.5872 (ppp) REVERT: F 363 LYS cc_start: 0.7556 (ttmt) cc_final: 0.6845 (ptpp) REVERT: F 509 LEU cc_start: 0.7634 (mm) cc_final: 0.7186 (mp) REVERT: F 616 MET cc_start: 0.7581 (mtp) cc_final: 0.7227 (mtp) REVERT: G 81 MET cc_start: 0.6653 (mtm) cc_final: 0.5995 (mmp) outliers start: 9 outliers final: 5 residues processed: 481 average time/residue: 0.7554 time to fit residues: 553.0892 Evaluate side-chains 376 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 371 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 226 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 74 ASN ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 621 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21924 Z= 0.257 Angle : 0.647 25.460 29768 Z= 0.345 Chirality : 0.039 0.164 3262 Planarity : 0.005 0.074 3750 Dihedral : 9.913 93.597 3206 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.20 % Favored : 92.65 % Rotamer: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.59 % 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: -2.30 (0.15), residues: 2598 helix: -0.14 (0.15), residues: 1058 sheet: -2.10 (0.31), residues: 252 loop : -2.67 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 577 HIS 0.005 0.001 HIS A 510 PHE 0.020 0.002 PHE F 495 TYR 0.020 0.002 TYR A 445 ARG 0.013 0.001 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 435 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 434 time to evaluate : 3.229 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: A 365 GLN cc_start: 0.7861 (mp10) cc_final: 0.7423 (mp10) REVERT: A 557 MET cc_start: 0.8022 (mmm) cc_final: 0.7753 (mmp) REVERT: B 321 MET cc_start: 0.6515 (mtp) cc_final: 0.6271 (mtp) REVERT: B 348 MET cc_start: 0.4700 (pmm) cc_final: 0.3856 (pmm) REVERT: B 501 PHE cc_start: 0.6624 (t80) cc_final: 0.6252 (t80) REVERT: B 523 MET cc_start: 0.7581 (tmm) cc_final: 0.7349 (tmm) REVERT: C 57 ILE cc_start: 0.7474 (mt) cc_final: 0.7272 (mt) REVERT: E 211 MET cc_start: 0.7025 (tmm) cc_final: 0.6471 (tmm) REVERT: E 327 GLU cc_start: 0.6436 (mm-30) cc_final: 0.6150 (mm-30) REVERT: E 661 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6844 (mp0) REVERT: F 312 ASN cc_start: 0.8047 (m110) cc_final: 0.7735 (m110) REVERT: F 362 MET cc_start: 0.6785 (ppp) cc_final: 0.5516 (ppp) REVERT: F 363 LYS cc_start: 0.7533 (ttmt) cc_final: 0.6966 (ptpp) REVERT: F 466 PHE cc_start: 0.7968 (t80) cc_final: 0.7623 (t80) REVERT: G 81 MET cc_start: 0.6934 (mtm) cc_final: 0.6199 (mmp) outliers start: 1 outliers final: 0 residues processed: 435 average time/residue: 0.7350 time to fit residues: 490.6022 Evaluate side-chains 347 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 175 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21924 Z= 0.282 Angle : 0.644 25.486 29768 Z= 0.344 Chirality : 0.039 0.267 3262 Planarity : 0.005 0.056 3750 Dihedral : 9.819 93.355 3206 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.81 % Favored : 91.07 % Rotamer: Outliers : 0.04 % Allowed : 2.41 % Favored : 97.55 % 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: -2.10 (0.16), residues: 2598 helix: 0.05 (0.15), residues: 1062 sheet: -1.78 (0.33), residues: 236 loop : -2.64 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 577 HIS 0.005 0.001 HIS E 326 PHE 0.033 0.002 PHE F 150 TYR 0.018 0.002 TYR E 305 ARG 0.014 0.000 ARG M 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 406 time to evaluate : 2.943 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: M 50 MET cc_start: 0.7298 (mtp) cc_final: 0.7003 (mtt) REVERT: O 11 MET cc_start: 0.7529 (ppp) cc_final: 0.7244 (ppp) REVERT: O 39 GLN cc_start: 0.7118 (tt0) cc_final: 0.6441 (tm-30) REVERT: A 365 GLN cc_start: 0.7830 (mp10) cc_final: 0.7467 (mp10) REVERT: A 479 ASP cc_start: 0.7889 (p0) cc_final: 0.7167 (p0) REVERT: A 557 MET cc_start: 0.8029 (mmm) cc_final: 0.7620 (mmt) REVERT: B 2 ASP cc_start: 0.6375 (t0) cc_final: 0.6149 (t0) REVERT: B 565 ASP cc_start: 0.8333 (p0) cc_final: 0.8121 (p0) REVERT: C 57 ILE cc_start: 0.7647 (mt) cc_final: 0.7417 (mt) REVERT: E 327 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6373 (mm-30) REVERT: E 401 ARG cc_start: 0.7087 (mmt180) cc_final: 0.6752 (mmt-90) REVERT: E 661 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6924 (mp0) REVERT: F 124 GLN cc_start: 0.7490 (mp10) cc_final: 0.7289 (mp10) REVERT: F 312 ASN cc_start: 0.8134 (m110) cc_final: 0.7779 (m110) REVERT: F 313 GLN cc_start: 0.7438 (mt0) cc_final: 0.7154 (mt0) REVERT: F 362 MET cc_start: 0.6858 (ppp) cc_final: 0.5560 (ppp) REVERT: F 363 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7087 (ptpp) REVERT: G 81 MET cc_start: 0.7004 (mtm) cc_final: 0.6262 (mmp) outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.7229 time to fit residues: 452.7107 Evaluate side-chains 332 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN F 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.8543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 21924 Z= 0.387 Angle : 0.715 25.608 29768 Z= 0.388 Chirality : 0.042 0.174 3262 Planarity : 0.006 0.104 3750 Dihedral : 9.975 95.805 3206 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.32 % Favored : 89.57 % Rotamer: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % 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: -2.31 (0.15), residues: 2598 helix: -0.06 (0.15), residues: 1048 sheet: -1.82 (0.33), residues: 244 loop : -2.82 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 577 HIS 0.008 0.002 HIS E 326 PHE 0.048 0.002 PHE B 466 TYR 0.024 0.002 TYR F 497 ARG 0.017 0.001 ARG E 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 364 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 362 time to evaluate : 2.770 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: O 11 MET cc_start: 0.7523 (ppp) cc_final: 0.7265 (ppp) REVERT: O 39 GLN cc_start: 0.7144 (tt0) cc_final: 0.6232 (tm-30) REVERT: A 365 GLN cc_start: 0.7846 (mp10) cc_final: 0.7565 (mp10) REVERT: A 464 TYR cc_start: 0.8024 (m-80) cc_final: 0.7463 (m-80) REVERT: A 557 MET cc_start: 0.8046 (mmm) cc_final: 0.7655 (mmt) REVERT: B 109 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7998 (tp30) REVERT: B 321 MET cc_start: 0.6565 (mtp) cc_final: 0.6333 (mtp) REVERT: B 324 TYR cc_start: 0.7096 (t80) cc_final: 0.6887 (t80) REVERT: C 57 ILE cc_start: 0.7925 (mt) cc_final: 0.7722 (mt) REVERT: E 672 LEU cc_start: 0.9141 (tp) cc_final: 0.8940 (tt) REVERT: F 88 VAL cc_start: 0.8827 (t) cc_final: 0.8624 (p) REVERT: F 166 PHE cc_start: 0.7864 (t80) cc_final: 0.7651 (t80) REVERT: F 312 ASN cc_start: 0.8026 (m110) cc_final: 0.7711 (m110) REVERT: F 362 MET cc_start: 0.7049 (ppp) cc_final: 0.5723 (ppp) REVERT: F 363 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7164 (ptpp) REVERT: G 54 LYS cc_start: 0.4825 (mmtt) cc_final: 0.4369 (mmtt) REVERT: G 81 MET cc_start: 0.6975 (mtm) cc_final: 0.6282 (mmm) outliers start: 2 outliers final: 1 residues processed: 363 average time/residue: 0.7096 time to fit residues: 396.5951 Evaluate side-chains 309 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 153 optimal weight: 0.0980 chunk 116 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 654 GLN B 664 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.8775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21924 Z= 0.199 Angle : 0.609 25.455 29768 Z= 0.322 Chirality : 0.038 0.360 3262 Planarity : 0.005 0.053 3750 Dihedral : 9.713 92.997 3206 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -1.89 (0.16), residues: 2598 helix: 0.37 (0.15), residues: 1048 sheet: -1.78 (0.33), residues: 236 loop : -2.62 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 437 HIS 0.009 0.001 HIS F 664 PHE 0.024 0.002 PHE B 466 TYR 0.020 0.001 TYR A 445 ARG 0.008 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 375 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.640 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: A 310 CYS cc_start: 0.8350 (m) cc_final: 0.8145 (m) REVERT: A 557 MET cc_start: 0.7945 (mmm) cc_final: 0.7491 (mmt) REVERT: B 2 ASP cc_start: 0.6834 (t0) cc_final: 0.6632 (t0) REVERT: B 109 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8002 (tp30) REVERT: E 661 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7585 (mt-10) REVERT: F 166 PHE cc_start: 0.7904 (t80) cc_final: 0.7660 (t80) REVERT: F 312 ASN cc_start: 0.8033 (m110) cc_final: 0.7663 (m110) REVERT: F 362 MET cc_start: 0.6963 (ppp) cc_final: 0.5667 (ppp) REVERT: F 363 LYS cc_start: 0.7727 (ttmt) cc_final: 0.6858 (ptpp) REVERT: G 81 MET cc_start: 0.6841 (mtm) cc_final: 0.6273 (mmm) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.7041 time to fit residues: 408.3462 Evaluate side-chains 304 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN M 77 ASN ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 664 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 425 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.9055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21924 Z= 0.250 Angle : 0.617 25.621 29768 Z= 0.328 Chirality : 0.038 0.169 3262 Planarity : 0.004 0.050 3750 Dihedral : 9.691 93.252 3206 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.97 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -1.82 (0.16), residues: 2598 helix: 0.45 (0.16), residues: 1048 sheet: -1.78 (0.33), residues: 236 loop : -2.60 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 437 HIS 0.004 0.001 HIS F 47 PHE 0.036 0.002 PHE B 150 TYR 0.026 0.001 TYR F 49 ARG 0.005 0.000 ARG M 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 357 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 3.355 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: A 310 CYS cc_start: 0.8312 (m) cc_final: 0.8035 (m) REVERT: A 557 MET cc_start: 0.7947 (mmm) cc_final: 0.7452 (mmt) REVERT: B 109 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8095 (tp30) REVERT: B 466 PHE cc_start: 0.8005 (t80) cc_final: 0.7776 (t80) REVERT: B 565 ASP cc_start: 0.8748 (p0) cc_final: 0.8452 (p0) REVERT: E 327 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6166 (mm-30) REVERT: E 595 MET cc_start: 0.8377 (tpp) cc_final: 0.8119 (tpp) REVERT: E 661 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7525 (mt-10) REVERT: E 672 LEU cc_start: 0.9339 (tt) cc_final: 0.9137 (tt) REVERT: F 166 PHE cc_start: 0.7908 (t80) cc_final: 0.7693 (t80) REVERT: F 312 ASN cc_start: 0.8078 (m110) cc_final: 0.7730 (m110) REVERT: F 362 MET cc_start: 0.7113 (ppp) cc_final: 0.5829 (ppp) REVERT: F 363 LYS cc_start: 0.7477 (ttmt) cc_final: 0.6925 (ptpp) REVERT: G 81 MET cc_start: 0.6864 (mtm) cc_final: 0.6292 (mmm) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.6999 time to fit residues: 387.6626 Evaluate side-chains 306 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 234 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.9418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21924 Z= 0.247 Angle : 0.620 25.607 29768 Z= 0.329 Chirality : 0.038 0.169 3262 Planarity : 0.005 0.066 3750 Dihedral : 9.668 93.201 3206 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.93 % Favored : 90.95 % Rotamer: Outliers : 0.04 % Allowed : 0.83 % Favored : 99.13 % 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: -1.71 (0.16), residues: 2598 helix: 0.57 (0.16), residues: 1044 sheet: -1.76 (0.34), residues: 236 loop : -2.55 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 98 HIS 0.004 0.001 HIS F 32 PHE 0.014 0.002 PHE F 9 TYR 0.020 0.002 TYR E 305 ARG 0.004 0.000 ARG M 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 346 time to evaluate : 3.286 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: A 310 CYS cc_start: 0.8333 (m) cc_final: 0.8037 (m) REVERT: A 557 MET cc_start: 0.7845 (mmm) cc_final: 0.7334 (mmt) REVERT: B 109 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8123 (tp30) REVERT: B 466 PHE cc_start: 0.8017 (t80) cc_final: 0.7747 (t80) REVERT: B 518 ASN cc_start: 0.9034 (p0) cc_final: 0.8721 (p0) REVERT: B 565 ASP cc_start: 0.8755 (p0) cc_final: 0.8438 (p0) REVERT: E 211 MET cc_start: 0.7177 (tmm) cc_final: 0.6956 (tmm) REVERT: E 595 MET cc_start: 0.8359 (tpp) cc_final: 0.8130 (tpp) REVERT: F 1 MET cc_start: 0.5859 (ttt) cc_final: 0.5561 (ttt) REVERT: F 166 PHE cc_start: 0.7970 (t80) cc_final: 0.7731 (t80) REVERT: F 302 ILE cc_start: 0.9075 (mp) cc_final: 0.8866 (mt) REVERT: F 312 ASN cc_start: 0.8156 (m110) cc_final: 0.7891 (m110) REVERT: F 362 MET cc_start: 0.7150 (ppp) cc_final: 0.5878 (ppp) REVERT: G 81 MET cc_start: 0.6890 (mtm) cc_final: 0.6240 (mmm) outliers start: 1 outliers final: 1 residues processed: 347 average time/residue: 0.6963 time to fit residues: 378.6158 Evaluate side-chains 298 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 ASN E 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.9628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21924 Z= 0.232 Angle : 0.610 25.569 29768 Z= 0.322 Chirality : 0.038 0.167 3262 Planarity : 0.004 0.063 3750 Dihedral : 9.617 92.846 3206 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.62 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.61 (0.16), residues: 2598 helix: 0.64 (0.16), residues: 1048 sheet: -1.60 (0.34), residues: 236 loop : -2.51 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP O 36 HIS 0.004 0.001 HIS F 32 PHE 0.028 0.002 PHE A 282 TYR 0.020 0.001 TYR F 49 ARG 0.005 0.000 ARG M 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Residue MET 477 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 669 is missing expected H atoms. Skipping. Residue MET 105 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 3.283 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: A 310 CYS cc_start: 0.8310 (m) cc_final: 0.8019 (m) REVERT: A 557 MET cc_start: 0.7767 (mmm) cc_final: 0.7237 (mmt) REVERT: B 109 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8140 (tp30) REVERT: B 466 PHE cc_start: 0.8024 (t80) cc_final: 0.7676 (t80) REVERT: B 518 ASN cc_start: 0.9016 (p0) cc_final: 0.8746 (p0) REVERT: E 688 GLU cc_start: 0.7362 (pp20) cc_final: 0.6713 (mm-30) REVERT: F 1 MET cc_start: 0.5999 (ttt) cc_final: 0.5709 (ttt) REVERT: F 166 PHE cc_start: 0.7989 (t80) cc_final: 0.7782 (t80) REVERT: F 174 MET cc_start: 0.6596 (tpt) cc_final: 0.6352 (tpt) REVERT: F 312 ASN cc_start: 0.8090 (m110) cc_final: 0.7785 (m110) REVERT: F 362 MET cc_start: 0.7229 (ppp) cc_final: 0.5877 (ppp) REVERT: F 363 LYS cc_start: 0.7424 (ttmt) cc_final: 0.6986 (ptpp) REVERT: G 81 MET cc_start: 0.6912 (mtm) cc_final: 0.6276 (mmm) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.7175 time to fit residues: 386.2118 Evaluate side-chains 295 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN B 425 ASN ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.158290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123077 restraints weight = 116969.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122771 restraints weight = 85556.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123517 restraints weight = 68912.525| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.9923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21924 Z= 0.260 Angle : 0.623 25.547 29768 Z= 0.330 Chirality : 0.038 0.178 3262 Planarity : 0.005 0.055 3750 Dihedral : 9.630 93.130 3206 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.97 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.61 (0.16), residues: 2598 helix: 0.63 (0.16), residues: 1058 sheet: -1.72 (0.34), residues: 236 loop : -2.50 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 98 HIS 0.004 0.001 HIS B 664 PHE 0.016 0.002 PHE B 512 TYR 0.020 0.002 TYR F 49 ARG 0.005 0.000 ARG F 563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9236.90 seconds wall clock time: 167 minutes 20.64 seconds (10040.64 seconds total)