Starting phenix.real_space_refine on Sun Feb 18 19:54:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udp_20742/02_2024/6udp_20742_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udp_20742/02_2024/6udp_20742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udp_20742/02_2024/6udp_20742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udp_20742/02_2024/6udp_20742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udp_20742/02_2024/6udp_20742_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udp_20742/02_2024/6udp_20742_updated.pdb" } resolution = 2.95 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= 0.042 sd= 3.333 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 144 5.16 5 C 14344 2.51 5 N 3864 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 11.89, per 1000 atoms: 0.52 Number of scatterers: 22728 At special positions: 0 Unit cell: (123.149, 123.149, 119.843, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 8 15.00 O 4368 8.00 N 3864 7.00 C 14344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 9.57 Conformation dependent library (CDL) restraints added in 4.6 seconds 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 32 sheets defined 33.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.76 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 No H-bonds generated for 'chain 'A' and resid 2 through 5' Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.558A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.626A pdb=" N TYR A 258 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.939A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.593A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'B' and resid 2 through 5 No H-bonds generated for 'chain 'B' and resid 2 through 5' Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.557A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.626A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 265 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.939A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.593A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'C' and resid 2 through 5 No H-bonds generated for 'chain 'C' and resid 2 through 5' Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.557A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.625A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN C 265 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 3.939A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 356 removed outlier: 3.592A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 495 through 499 Processing helix chain 'D' and resid 2 through 5 No H-bonds generated for 'chain 'D' and resid 2 through 5' Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.557A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.625A pdb=" N TYR D 258 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN D 265 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.938A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 356 removed outlier: 3.593A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'E' and resid 2 through 5 No H-bonds generated for 'chain 'E' and resid 2 through 5' Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.557A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.625A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN E 265 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.940A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 356 removed outlier: 3.592A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'E' and resid 495 through 499 Processing helix chain 'F' and resid 2 through 5 No H-bonds generated for 'chain 'F' and resid 2 through 5' Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.557A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.625A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN F 265 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.939A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 356 removed outlier: 3.593A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'G' and resid 2 through 5 No H-bonds generated for 'chain 'G' and resid 2 through 5' Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.557A pdb=" N ALA G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.626A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN G 265 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 3.939A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 356 removed outlier: 3.593A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'G' and resid 495 through 499 Processing helix chain 'H' and resid 2 through 5 No H-bonds generated for 'chain 'H' and resid 2 through 5' Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.556A pdb=" N ALA H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.626A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN H 265 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.939A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 356 removed outlier: 3.593A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 499 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 5.734A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 383 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.700A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.734A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.701A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 400 through 402 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 5.733A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.700A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 400 through 402 Processing sheet with id= M, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'D' and resid 65 through 67 removed outlier: 5.734A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.700A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 400 through 402 Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'E' and resid 65 through 67 removed outlier: 5.733A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR E 383 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.700A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 400 through 402 Processing sheet with id= U, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'F' and resid 65 through 67 removed outlier: 5.733A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR F 383 " --> pdb=" O VAL F 361 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.700A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 400 through 402 Processing sheet with id= Y, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'G' and resid 65 through 67 removed outlier: 5.733A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.701A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 400 through 402 Processing sheet with id= AC, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.733A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR H 383 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.701A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 400 through 402 608 hydrogen bonds defined for protein. 1632 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: 7.15 Time building geometry restraints manager: 10.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3816 1.31 - 1.43: 5679 1.43 - 1.56: 13337 1.56 - 1.68: 24 1.68 - 1.80: 240 Bond restraints: 23096 Sorted by residual: bond pdb=" C4 IMP C 601 " pdb=" N3 IMP C 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C4 IMP E 601 " pdb=" N3 IMP E 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP F 601 " pdb=" N3 IMP F 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP D 601 " pdb=" N3 IMP D 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP B 601 " pdb=" N3 IMP B 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.67e+01 ... (remaining 23091 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.70: 416 105.70 - 112.55: 11592 112.55 - 119.41: 7503 119.41 - 126.26: 11525 126.26 - 133.12: 172 Bond angle restraints: 31208 Sorted by residual: angle pdb=" CA LEU G 235 " pdb=" CB LEU G 235 " pdb=" CG LEU G 235 " ideal model delta sigma weight residual 116.30 131.22 -14.92 3.50e+00 8.16e-02 1.82e+01 angle pdb=" CA LEU D 235 " pdb=" CB LEU D 235 " pdb=" CG LEU D 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU C 235 " pdb=" CB LEU C 235 " pdb=" CG LEU C 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU H 235 " pdb=" CB LEU H 235 " pdb=" CG LEU H 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU E 235 " pdb=" CB LEU E 235 " pdb=" CG LEU E 235 " ideal model delta sigma weight residual 116.30 131.16 -14.86 3.50e+00 8.16e-02 1.80e+01 ... (remaining 31203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 13696 35.14 - 70.27: 100 70.27 - 105.41: 8 105.41 - 140.55: 0 140.55 - 175.68: 4 Dihedral angle restraints: 13808 sinusoidal: 5304 harmonic: 8504 Sorted by residual: dihedral pdb=" C5' IMP C 601 " pdb=" O5' IMP C 601 " pdb=" P IMP C 601 " pdb=" O2P IMP C 601 " ideal model delta sinusoidal sigma weight residual -168.07 7.61 -175.68 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' IMP B 601 " pdb=" O5' IMP B 601 " pdb=" P IMP B 601 " pdb=" O2P IMP B 601 " ideal model delta sinusoidal sigma weight residual -168.07 7.57 -175.64 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' IMP A 601 " pdb=" O5' IMP A 601 " pdb=" P IMP A 601 " pdb=" O2P IMP A 601 " ideal model delta sinusoidal sigma weight residual -168.07 7.52 -175.59 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 13805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2573 0.055 - 0.110: 850 0.110 - 0.165: 125 0.165 - 0.219: 28 0.219 - 0.274: 16 Chirality restraints: 3592 Sorted by residual: chirality pdb=" C3' IMP G 601 " pdb=" C2' IMP G 601 " pdb=" C4' IMP G 601 " pdb=" O3' IMP G 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' IMP C 601 " pdb=" C2' IMP C 601 " pdb=" C4' IMP C 601 " pdb=" O3' IMP C 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' IMP H 601 " pdb=" C2' IMP H 601 " pdb=" C4' IMP H 601 " pdb=" O3' IMP H 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3589 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 233 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO E 234 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 234 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 234 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 233 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 234 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 233 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO G 234 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 234 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 234 " 0.031 5.00e-02 4.00e+02 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7578 2.85 - 3.36: 20970 3.36 - 3.88: 39232 3.88 - 4.39: 45930 4.39 - 4.90: 79201 Nonbonded interactions: 192911 Sorted by model distance: nonbonded pdb=" OD1 ASN H 25 " pdb=" NZ LYS H 349 " model vdw 2.340 2.520 nonbonded pdb=" OD1 ASN C 25 " pdb=" NZ LYS C 349 " model vdw 2.340 2.520 nonbonded pdb=" OD1 ASN E 25 " pdb=" NZ LYS E 349 " model vdw 2.340 2.520 nonbonded pdb=" OD1 ASN A 25 " pdb=" NZ LYS A 349 " model vdw 2.340 2.520 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 349 " model vdw 2.340 2.520 ... (remaining 192906 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.180 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 62.830 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.007 0.137 23096 Z= 0.480 Angle : 0.871 14.920 31208 Z= 0.460 Chirality : 0.056 0.274 3592 Planarity : 0.006 0.053 3976 Dihedral : 10.711 175.684 8416 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.67 % Allowed : 5.03 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.38 (0.12), residues: 2960 helix: -2.87 (0.10), residues: 1104 sheet: -1.67 (0.23), residues: 424 loop : -1.77 (0.13), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 93 PHE 0.017 0.003 PHE E 401 TYR 0.020 0.003 TYR E 484 ARG 0.004 0.001 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 491 time to evaluate : 2.560 Fit side-chains REVERT: A 58 LYS cc_start: 0.8761 (mttp) cc_final: 0.8429 (mtmt) REVERT: A 474 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8169 (mtmt) REVERT: B 58 LYS cc_start: 0.8775 (mttp) cc_final: 0.8408 (mtmt) REVERT: C 36 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8621 (pp) REVERT: C 58 LYS cc_start: 0.8729 (mttp) cc_final: 0.8424 (mtmt) REVERT: C 71 ASP cc_start: 0.8953 (p0) cc_final: 0.8745 (p0) REVERT: D 36 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8464 (pp) REVERT: D 474 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8011 (mtmt) REVERT: E 36 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8623 (pp) REVERT: E 58 LYS cc_start: 0.8787 (mttp) cc_final: 0.8475 (mtmt) REVERT: E 474 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8183 (mtmt) REVERT: F 50 ASP cc_start: 0.8295 (t70) cc_final: 0.8011 (t0) REVERT: F 58 LYS cc_start: 0.8829 (mttp) cc_final: 0.8477 (mtmt) REVERT: F 474 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8091 (mtmt) REVERT: G 50 ASP cc_start: 0.8202 (t70) cc_final: 0.7964 (t0) REVERT: G 58 LYS cc_start: 0.8788 (mttp) cc_final: 0.8519 (mtmt) REVERT: G 483 MET cc_start: 0.9120 (tmm) cc_final: 0.8898 (tmm) REVERT: H 58 LYS cc_start: 0.8793 (mttp) cc_final: 0.8425 (mtmt) REVERT: H 483 MET cc_start: 0.9152 (tmm) cc_final: 0.8943 (tmm) outliers start: 16 outliers final: 0 residues processed: 501 average time/residue: 1.2387 time to fit residues: 715.3102 Evaluate side-chains 320 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 317 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 36 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.3980 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 232 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN A 343 GLN B 48 GLN B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 343 GLN B 368 GLN C 48 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 334 GLN C 343 GLN C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 334 GLN D 343 GLN D 368 GLN E 48 GLN E 334 GLN E 343 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 343 GLN G 48 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN G 343 GLN ** G 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN H 343 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23096 Z= 0.172 Angle : 0.465 8.011 31208 Z= 0.246 Chirality : 0.041 0.159 3592 Planarity : 0.004 0.035 3976 Dihedral : 7.492 147.860 3294 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.23 % Allowed : 12.25 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.87 (0.14), residues: 2960 helix: -1.07 (0.14), residues: 1088 sheet: -1.17 (0.23), residues: 424 loop : -1.30 (0.14), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 504 PHE 0.012 0.001 PHE B 401 TYR 0.011 0.001 TYR C 353 ARG 0.002 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 366 time to evaluate : 2.622 Fit side-chains REVERT: A 21 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8240 (tt0) REVERT: A 50 ASP cc_start: 0.8129 (t70) cc_final: 0.7879 (t0) REVERT: A 58 LYS cc_start: 0.8754 (mttp) cc_final: 0.8480 (mtmt) REVERT: A 71 ASP cc_start: 0.8967 (p0) cc_final: 0.8766 (p0) REVERT: A 235 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7391 (pp) REVERT: A 245 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 474 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8110 (mtpt) REVERT: A 510 GLU cc_start: 0.5721 (tp30) cc_final: 0.4685 (pt0) REVERT: B 50 ASP cc_start: 0.8185 (t70) cc_final: 0.7937 (t0) REVERT: B 58 LYS cc_start: 0.8757 (mttp) cc_final: 0.8398 (mtmt) REVERT: B 510 GLU cc_start: 0.5731 (tp30) cc_final: 0.4885 (pt0) REVERT: C 36 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7772 (mt) REVERT: C 50 ASP cc_start: 0.8135 (t70) cc_final: 0.7898 (t0) REVERT: C 58 LYS cc_start: 0.8798 (mttp) cc_final: 0.8508 (mtmt) REVERT: C 235 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7462 (pp) REVERT: C 510 GLU cc_start: 0.5762 (tp30) cc_final: 0.4646 (pt0) REVERT: D 36 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8485 (pp) REVERT: D 50 ASP cc_start: 0.8180 (t70) cc_final: 0.7914 (t0) REVERT: D 58 LYS cc_start: 0.8790 (mttp) cc_final: 0.8419 (mtmt) REVERT: D 235 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7495 (pp) REVERT: D 474 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7994 (mtmt) REVERT: D 510 GLU cc_start: 0.5609 (tp30) cc_final: 0.4631 (pt0) REVERT: E 36 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7706 (mt) REVERT: E 50 ASP cc_start: 0.8124 (t70) cc_final: 0.7844 (t0) REVERT: E 58 LYS cc_start: 0.8773 (mttp) cc_final: 0.8494 (mtmt) REVERT: E 235 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7389 (pp) REVERT: E 474 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8140 (mtmt) REVERT: E 510 GLU cc_start: 0.5689 (tp30) cc_final: 0.4554 (pt0) REVERT: F 50 ASP cc_start: 0.8208 (t70) cc_final: 0.7892 (t0) REVERT: F 58 LYS cc_start: 0.8824 (mttp) cc_final: 0.8496 (mtmt) REVERT: F 235 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7474 (pp) REVERT: F 474 LYS cc_start: 0.8298 (mtpt) cc_final: 0.8030 (mtmt) REVERT: F 510 GLU cc_start: 0.5709 (tp30) cc_final: 0.4814 (pt0) REVERT: G 50 ASP cc_start: 0.8117 (t70) cc_final: 0.7805 (t0) REVERT: G 58 LYS cc_start: 0.8750 (mttp) cc_final: 0.8481 (mtmt) REVERT: G 235 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7407 (pp) REVERT: G 474 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8113 (mtpt) REVERT: H 50 ASP cc_start: 0.8205 (t70) cc_final: 0.7963 (t0) REVERT: H 58 LYS cc_start: 0.8781 (mttp) cc_final: 0.8443 (mtmt) REVERT: H 235 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7561 (pp) REVERT: H 510 GLU cc_start: 0.5695 (tp30) cc_final: 0.4773 (pt0) outliers start: 77 outliers final: 21 residues processed: 417 average time/residue: 1.1098 time to fit residues: 538.8097 Evaluate side-chains 341 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 309 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN C 265 GLN C 303 ASN C 334 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN E 48 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN G 48 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23096 Z= 0.279 Angle : 0.499 7.644 31208 Z= 0.259 Chirality : 0.043 0.152 3592 Planarity : 0.004 0.036 3976 Dihedral : 6.183 75.876 3294 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.29 % Allowed : 10.36 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.39 (0.14), residues: 2960 helix: -0.64 (0.15), residues: 1104 sheet: -0.94 (0.23), residues: 464 loop : -1.01 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 504 PHE 0.010 0.002 PHE F 401 TYR 0.013 0.002 TYR B 353 ARG 0.003 0.001 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 320 time to evaluate : 2.463 Fit side-chains REVERT: A 21 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8337 (tt0) REVERT: A 36 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8487 (pp) REVERT: A 58 LYS cc_start: 0.8716 (mttp) cc_final: 0.8426 (mtmt) REVERT: A 235 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7374 (pp) REVERT: A 474 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8086 (mtmt) REVERT: A 510 GLU cc_start: 0.6062 (tp30) cc_final: 0.4815 (pt0) REVERT: B 36 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8536 (pp) REVERT: B 50 ASP cc_start: 0.8139 (t70) cc_final: 0.7849 (t0) REVERT: B 58 LYS cc_start: 0.8744 (mttp) cc_final: 0.8393 (mtmt) REVERT: B 510 GLU cc_start: 0.6052 (tp30) cc_final: 0.4935 (pt0) REVERT: C 36 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8239 (pp) REVERT: C 58 LYS cc_start: 0.8761 (mttp) cc_final: 0.8473 (mtmt) REVERT: C 235 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7488 (pp) REVERT: C 492 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8304 (mtpp) REVERT: C 510 GLU cc_start: 0.6103 (tp30) cc_final: 0.4788 (pt0) REVERT: D 21 GLN cc_start: 0.8791 (tt0) cc_final: 0.8415 (tt0) REVERT: D 36 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8518 (pp) REVERT: D 50 ASP cc_start: 0.8211 (t70) cc_final: 0.7939 (t0) REVERT: D 58 LYS cc_start: 0.8758 (mttp) cc_final: 0.8393 (mtmt) REVERT: D 235 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7456 (pp) REVERT: D 288 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7988 (mttt) REVERT: D 478 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: D 510 GLU cc_start: 0.6042 (tp30) cc_final: 0.4804 (pt0) REVERT: E 36 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8122 (pp) REVERT: E 50 ASP cc_start: 0.8137 (t70) cc_final: 0.7828 (t0) REVERT: E 58 LYS cc_start: 0.8733 (mttp) cc_final: 0.8472 (mtmt) REVERT: E 235 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7440 (pp) REVERT: E 474 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8117 (mtmt) REVERT: E 492 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8241 (mtpp) REVERT: E 510 GLU cc_start: 0.6030 (tp30) cc_final: 0.4744 (pt0) REVERT: F 50 ASP cc_start: 0.8191 (t70) cc_final: 0.7909 (t0) REVERT: F 58 LYS cc_start: 0.8790 (mttp) cc_final: 0.8475 (mtmt) REVERT: F 235 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7443 (pp) REVERT: F 510 GLU cc_start: 0.6083 (tp30) cc_final: 0.4834 (pt0) REVERT: G 36 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8491 (pp) REVERT: G 50 ASP cc_start: 0.8113 (t70) cc_final: 0.7824 (t0) REVERT: G 58 LYS cc_start: 0.8740 (mttp) cc_final: 0.8488 (mtmt) REVERT: G 235 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7381 (pp) REVERT: G 492 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8326 (mtpp) REVERT: G 510 GLU cc_start: 0.6062 (tp30) cc_final: 0.4794 (pt0) REVERT: H 36 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8442 (pp) REVERT: H 50 ASP cc_start: 0.8157 (t70) cc_final: 0.7898 (t0) REVERT: H 58 LYS cc_start: 0.8768 (mttp) cc_final: 0.8439 (mtmt) REVERT: H 235 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7516 (pp) REVERT: H 492 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8267 (mtpp) REVERT: H 510 GLU cc_start: 0.6004 (tp30) cc_final: 0.4916 (pt0) outliers start: 126 outliers final: 45 residues processed: 399 average time/residue: 1.2627 time to fit residues: 584.4525 Evaluate side-chains 377 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 312 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 478 GLN Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 492 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 0.4980 chunk 202 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 256 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN B 303 ASN B 334 GLN C 265 GLN C 303 ASN C 334 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 334 GLN E 48 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN G 48 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 48 GLN H 283 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23096 Z= 0.228 Angle : 0.472 7.332 31208 Z= 0.246 Chirality : 0.042 0.147 3592 Planarity : 0.004 0.036 3976 Dihedral : 5.773 53.636 3294 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.03 % Allowed : 11.91 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.07 (0.14), residues: 2960 helix: -0.37 (0.15), residues: 1112 sheet: -0.85 (0.23), residues: 464 loop : -0.80 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 504 PHE 0.011 0.001 PHE F 401 TYR 0.011 0.001 TYR B 353 ARG 0.002 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 315 time to evaluate : 2.724 Fit side-chains REVERT: A 58 LYS cc_start: 0.8706 (mttp) cc_final: 0.8422 (mtmt) REVERT: A 235 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7327 (pp) REVERT: A 474 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8125 (mtmt) REVERT: A 510 GLU cc_start: 0.6240 (tp30) cc_final: 0.4936 (pt0) REVERT: B 50 ASP cc_start: 0.8154 (t70) cc_final: 0.7858 (t0) REVERT: B 58 LYS cc_start: 0.8739 (mttp) cc_final: 0.8382 (mtmt) REVERT: B 510 GLU cc_start: 0.6285 (tp30) cc_final: 0.5121 (pt0) REVERT: C 21 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8377 (tt0) REVERT: C 36 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7867 (mt) REVERT: C 50 ASP cc_start: 0.8149 (t70) cc_final: 0.7853 (t0) REVERT: C 58 LYS cc_start: 0.8770 (mttp) cc_final: 0.8496 (mtmt) REVERT: C 235 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7375 (pp) REVERT: C 510 GLU cc_start: 0.6346 (tp30) cc_final: 0.5014 (pt0) REVERT: D 36 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8424 (pp) REVERT: D 50 ASP cc_start: 0.8193 (t70) cc_final: 0.7889 (t0) REVERT: D 58 LYS cc_start: 0.8724 (mttp) cc_final: 0.8374 (mtmt) REVERT: D 235 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7404 (pp) REVERT: D 288 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7951 (mttt) REVERT: D 441 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: D 510 GLU cc_start: 0.6206 (tp30) cc_final: 0.5044 (pt0) REVERT: E 36 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7831 (mt) REVERT: E 50 ASP cc_start: 0.8156 (t70) cc_final: 0.7836 (t0) REVERT: E 58 LYS cc_start: 0.8740 (mttp) cc_final: 0.8477 (mtmt) REVERT: E 235 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7361 (pp) REVERT: E 510 GLU cc_start: 0.6238 (tp30) cc_final: 0.4919 (pt0) REVERT: F 50 ASP cc_start: 0.8200 (t70) cc_final: 0.7908 (t0) REVERT: F 58 LYS cc_start: 0.8797 (mttp) cc_final: 0.8479 (mtmt) REVERT: F 235 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7391 (pp) REVERT: F 492 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8186 (mtpp) REVERT: F 510 GLU cc_start: 0.6209 (tp30) cc_final: 0.4947 (pt0) REVERT: G 50 ASP cc_start: 0.8150 (t70) cc_final: 0.7868 (t0) REVERT: G 58 LYS cc_start: 0.8763 (mttp) cc_final: 0.8498 (mtmt) REVERT: G 235 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7324 (pp) REVERT: G 254 GLU cc_start: 0.8163 (tp30) cc_final: 0.7797 (tp30) REVERT: G 510 GLU cc_start: 0.6246 (tp30) cc_final: 0.4913 (pt0) REVERT: H 36 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8261 (pp) REVERT: H 50 ASP cc_start: 0.8178 (t70) cc_final: 0.7897 (t0) REVERT: H 58 LYS cc_start: 0.8769 (mttp) cc_final: 0.8444 (mtmt) REVERT: H 235 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7493 (pp) REVERT: H 510 GLU cc_start: 0.6241 (tp30) cc_final: 0.5091 (pt0) outliers start: 120 outliers final: 63 residues processed: 387 average time/residue: 1.1975 time to fit residues: 538.2119 Evaluate side-chains 370 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 293 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 256 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN C 265 GLN C 283 GLN C 303 ASN C 334 GLN D 303 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23096 Z= 0.194 Angle : 0.458 5.695 31208 Z= 0.238 Chirality : 0.042 0.143 3592 Planarity : 0.004 0.036 3976 Dihedral : 5.598 52.628 3294 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.19 % Allowed : 13.26 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.83 (0.15), residues: 2960 helix: -0.26 (0.15), residues: 1160 sheet: -0.73 (0.25), residues: 360 loop : -0.62 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 504 PHE 0.010 0.001 PHE E 401 TYR 0.009 0.001 TYR F 353 ARG 0.002 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 315 time to evaluate : 2.617 Fit side-chains REVERT: A 58 LYS cc_start: 0.8721 (mttp) cc_final: 0.8433 (mtmt) REVERT: A 109 LYS cc_start: 0.8330 (mptp) cc_final: 0.8124 (mptp) REVERT: A 235 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7306 (pp) REVERT: A 441 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: A 474 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8122 (mtmt) REVERT: A 510 GLU cc_start: 0.6293 (tp30) cc_final: 0.4978 (pt0) REVERT: B 50 ASP cc_start: 0.8158 (t70) cc_final: 0.7865 (t0) REVERT: B 58 LYS cc_start: 0.8738 (mttp) cc_final: 0.8378 (mtmt) REVERT: B 235 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7427 (pp) REVERT: B 510 GLU cc_start: 0.6285 (tp30) cc_final: 0.5111 (pt0) REVERT: C 21 GLN cc_start: 0.8713 (tt0) cc_final: 0.8368 (tt0) REVERT: C 36 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8131 (pp) REVERT: C 50 ASP cc_start: 0.8148 (t70) cc_final: 0.7851 (t0) REVERT: C 58 LYS cc_start: 0.8781 (mttp) cc_final: 0.8509 (mtmt) REVERT: C 235 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7346 (pp) REVERT: C 492 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8165 (mtpp) REVERT: C 510 GLU cc_start: 0.6346 (tp30) cc_final: 0.5960 (tp30) REVERT: D 36 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8320 (pp) REVERT: D 50 ASP cc_start: 0.8191 (t70) cc_final: 0.7892 (t0) REVERT: D 58 LYS cc_start: 0.8732 (mttp) cc_final: 0.8381 (mtmt) REVERT: D 235 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7430 (pp) REVERT: D 441 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: D 510 GLU cc_start: 0.6202 (tp30) cc_final: 0.4991 (pt0) REVERT: E 50 ASP cc_start: 0.8156 (t70) cc_final: 0.7835 (t0) REVERT: E 58 LYS cc_start: 0.8772 (mttp) cc_final: 0.8520 (mtmt) REVERT: E 235 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7353 (pp) REVERT: E 492 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8219 (mtpp) REVERT: E 510 GLU cc_start: 0.6242 (tp30) cc_final: 0.4953 (pt0) REVERT: F 50 ASP cc_start: 0.8209 (t70) cc_final: 0.7916 (t0) REVERT: F 58 LYS cc_start: 0.8796 (mttp) cc_final: 0.8478 (mtmt) REVERT: F 235 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7399 (pp) REVERT: F 492 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8094 (mtpt) REVERT: F 510 GLU cc_start: 0.6186 (tp30) cc_final: 0.4978 (pt0) REVERT: G 50 ASP cc_start: 0.8158 (t70) cc_final: 0.7868 (t0) REVERT: G 58 LYS cc_start: 0.8782 (mttp) cc_final: 0.8525 (mtmt) REVERT: G 235 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7327 (pp) REVERT: G 410 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7815 (tppp) REVERT: G 492 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8082 (mtpp) REVERT: G 510 GLU cc_start: 0.6296 (tp30) cc_final: 0.4988 (pt0) REVERT: H 36 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8305 (pp) REVERT: H 50 ASP cc_start: 0.8188 (t70) cc_final: 0.7898 (t0) REVERT: H 58 LYS cc_start: 0.8759 (mttp) cc_final: 0.8434 (mtmt) REVERT: H 235 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7506 (pp) REVERT: H 492 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: H 510 GLU cc_start: 0.6219 (tp30) cc_final: 0.5078 (pt0) outliers start: 100 outliers final: 57 residues processed: 379 average time/residue: 1.2692 time to fit residues: 555.7784 Evaluate side-chains 371 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 296 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 492 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 167 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 150 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN C 265 GLN C 303 ASN C 309 GLN C 334 GLN D 303 ASN D 334 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23096 Z= 0.167 Angle : 0.447 5.701 31208 Z= 0.231 Chirality : 0.041 0.141 3592 Planarity : 0.003 0.036 3976 Dihedral : 5.352 50.902 3292 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.49 % Allowed : 13.59 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.57 (0.15), residues: 2960 helix: -0.01 (0.15), residues: 1152 sheet: -0.67 (0.26), residues: 360 loop : -0.47 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 504 PHE 0.010 0.001 PHE C 401 TYR 0.008 0.001 TYR E 353 ARG 0.002 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 301 time to evaluate : 2.564 Fit side-chains REVERT: A 21 GLN cc_start: 0.8661 (tt0) cc_final: 0.8333 (tt0) REVERT: A 58 LYS cc_start: 0.8728 (mttp) cc_final: 0.8440 (mtmt) REVERT: A 235 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7240 (pp) REVERT: A 441 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: A 474 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8134 (mtmt) REVERT: A 510 GLU cc_start: 0.6291 (tp30) cc_final: 0.5024 (pt0) REVERT: B 50 ASP cc_start: 0.8160 (t70) cc_final: 0.7880 (t0) REVERT: B 58 LYS cc_start: 0.8734 (mttp) cc_final: 0.8372 (mtmt) REVERT: B 235 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7431 (pp) REVERT: B 510 GLU cc_start: 0.6263 (tp30) cc_final: 0.5914 (tp30) REVERT: C 21 GLN cc_start: 0.8690 (tt0) cc_final: 0.8344 (tt0) REVERT: C 36 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7883 (mt) REVERT: C 50 ASP cc_start: 0.8151 (t70) cc_final: 0.7842 (t0) REVERT: C 58 LYS cc_start: 0.8780 (mttp) cc_final: 0.8508 (mtmt) REVERT: C 235 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7322 (pp) REVERT: C 492 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8155 (mtpp) REVERT: C 510 GLU cc_start: 0.6327 (tp30) cc_final: 0.5032 (pt0) REVERT: D 36 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8135 (pp) REVERT: D 50 ASP cc_start: 0.8199 (t70) cc_final: 0.7909 (t0) REVERT: D 58 LYS cc_start: 0.8739 (mttp) cc_final: 0.8388 (mtmt) REVERT: D 235 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7417 (pp) REVERT: D 441 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6746 (mp10) REVERT: D 510 GLU cc_start: 0.6226 (tp30) cc_final: 0.5089 (pt0) REVERT: E 36 LEU cc_start: 0.8106 (pp) cc_final: 0.7711 (mt) REVERT: E 50 ASP cc_start: 0.8154 (t70) cc_final: 0.7831 (t0) REVERT: E 58 LYS cc_start: 0.8785 (mttp) cc_final: 0.8545 (mtmt) REVERT: E 235 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7345 (pp) REVERT: E 492 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8173 (mtpp) REVERT: E 510 GLU cc_start: 0.6213 (tp30) cc_final: 0.4985 (pt0) REVERT: F 36 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7988 (pp) REVERT: F 50 ASP cc_start: 0.8198 (t70) cc_final: 0.7919 (t0) REVERT: F 58 LYS cc_start: 0.8792 (mttp) cc_final: 0.8471 (mtmt) REVERT: F 235 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7402 (pp) REVERT: F 492 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8103 (mtpp) REVERT: F 510 GLU cc_start: 0.6183 (tp30) cc_final: 0.5021 (pt0) REVERT: G 50 ASP cc_start: 0.8156 (t70) cc_final: 0.7856 (t0) REVERT: G 58 LYS cc_start: 0.8780 (mttp) cc_final: 0.8533 (mtmt) REVERT: G 235 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7291 (pp) REVERT: G 410 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7808 (tppp) REVERT: G 492 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8113 (mtpp) REVERT: G 510 GLU cc_start: 0.6263 (tp30) cc_final: 0.4976 (pt0) REVERT: H 50 ASP cc_start: 0.8180 (t70) cc_final: 0.7906 (t0) REVERT: H 58 LYS cc_start: 0.8762 (mttp) cc_final: 0.8432 (mtmt) REVERT: H 235 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7458 (pp) REVERT: H 453 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7728 (tt) REVERT: H 492 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8134 (mtpp) REVERT: H 510 GLU cc_start: 0.6206 (tp30) cc_final: 0.5112 (pt0) outliers start: 107 outliers final: 57 residues processed: 367 average time/residue: 1.2335 time to fit residues: 523.5833 Evaluate side-chains 370 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 294 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 492 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 283 GLN B 303 ASN B 334 GLN C 265 GLN C 303 ASN C 334 GLN D 303 ASN E 309 GLN E 334 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23096 Z= 0.359 Angle : 0.529 6.036 31208 Z= 0.275 Chirality : 0.045 0.147 3592 Planarity : 0.004 0.035 3976 Dihedral : 5.699 53.374 3292 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.78 % Allowed : 13.88 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.80 (0.15), residues: 2960 helix: -0.20 (0.15), residues: 1152 sheet: -0.82 (0.24), residues: 376 loop : -0.58 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 93 PHE 0.010 0.002 PHE F 401 TYR 0.012 0.002 TYR B 348 ARG 0.003 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 289 time to evaluate : 2.420 Fit side-chains REVERT: A 21 GLN cc_start: 0.8769 (tt0) cc_final: 0.8460 (tt0) REVERT: A 50 ASP cc_start: 0.8184 (t70) cc_final: 0.7879 (t0) REVERT: A 58 LYS cc_start: 0.8785 (mttp) cc_final: 0.8499 (mtmt) REVERT: A 235 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7290 (pp) REVERT: A 441 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7005 (mp10) REVERT: A 453 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 510 GLU cc_start: 0.6370 (tp30) cc_final: 0.4962 (pt0) REVERT: B 50 ASP cc_start: 0.8206 (t70) cc_final: 0.7888 (t0) REVERT: B 58 LYS cc_start: 0.8758 (mttp) cc_final: 0.8390 (mtmt) REVERT: B 235 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7491 (pp) REVERT: B 510 GLU cc_start: 0.6330 (tp30) cc_final: 0.5083 (pt0) REVERT: C 36 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8135 (pp) REVERT: C 58 LYS cc_start: 0.8819 (mttp) cc_final: 0.8543 (mtmt) REVERT: C 235 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7339 (pp) REVERT: C 412 ARG cc_start: 0.8568 (ptt90) cc_final: 0.8363 (ptt90) REVERT: C 453 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8086 (tt) REVERT: C 492 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: D 21 GLN cc_start: 0.8809 (tt0) cc_final: 0.8489 (tt0) REVERT: D 36 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8098 (pp) REVERT: D 58 LYS cc_start: 0.8807 (mttp) cc_final: 0.8463 (mtmt) REVERT: D 235 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7427 (pp) REVERT: D 441 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: D 453 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8030 (tt) REVERT: D 510 GLU cc_start: 0.6257 (tp30) cc_final: 0.4983 (pt0) REVERT: D 512 ARG cc_start: 0.5341 (mmt180) cc_final: 0.5121 (mmt90) REVERT: E 58 LYS cc_start: 0.8810 (mttp) cc_final: 0.8551 (mtmt) REVERT: E 235 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7359 (pp) REVERT: E 412 ARG cc_start: 0.8542 (ptt90) cc_final: 0.8303 (ptt90) REVERT: E 492 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: E 510 GLU cc_start: 0.6379 (tp30) cc_final: 0.4988 (pt0) REVERT: F 7 SER cc_start: 0.8960 (t) cc_final: 0.8729 (t) REVERT: F 36 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8101 (pp) REVERT: F 58 LYS cc_start: 0.8853 (mttp) cc_final: 0.8526 (mtmt) REVERT: F 235 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7388 (pp) REVERT: F 492 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8216 (mtpp) REVERT: F 510 GLU cc_start: 0.6237 (tp30) cc_final: 0.4931 (pt0) REVERT: G 50 ASP cc_start: 0.8199 (t70) cc_final: 0.7921 (t0) REVERT: G 58 LYS cc_start: 0.8821 (mttp) cc_final: 0.8564 (mtmt) REVERT: G 235 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7331 (pp) REVERT: G 492 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8066 (mtpt) REVERT: G 510 GLU cc_start: 0.6236 (tp30) cc_final: 0.4865 (pt0) REVERT: H 50 ASP cc_start: 0.8228 (t70) cc_final: 0.7931 (t0) REVERT: H 58 LYS cc_start: 0.8827 (mttp) cc_final: 0.8494 (mtmt) REVERT: H 235 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7442 (pp) REVERT: H 453 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7884 (tt) REVERT: H 492 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8136 (mtpt) REVERT: H 510 GLU cc_start: 0.6302 (tp30) cc_final: 0.5082 (pt0) outliers start: 114 outliers final: 68 residues processed: 365 average time/residue: 1.2874 time to fit residues: 541.0824 Evaluate side-chains 367 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 277 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 492 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 303 ASN B 334 GLN C 265 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN E 334 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN F 303 ASN F 334 GLN F 478 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23096 Z= 0.209 Angle : 0.476 7.590 31208 Z= 0.244 Chirality : 0.042 0.144 3592 Planarity : 0.004 0.035 3976 Dihedral : 5.329 51.567 3292 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.53 % Allowed : 14.97 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.61 (0.15), residues: 2960 helix: -0.05 (0.15), residues: 1160 sheet: -0.80 (0.25), residues: 360 loop : -0.45 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 504 PHE 0.010 0.001 PHE B 401 TYR 0.009 0.001 TYR G 348 ARG 0.002 0.000 ARG H 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 284 time to evaluate : 2.668 Fit side-chains REVERT: A 50 ASP cc_start: 0.8180 (t70) cc_final: 0.7863 (t0) REVERT: A 58 LYS cc_start: 0.8733 (mttp) cc_final: 0.8467 (mtmt) REVERT: A 235 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7223 (pp) REVERT: A 277 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: A 441 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.6724 (mp10) REVERT: A 453 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 510 GLU cc_start: 0.6337 (tp30) cc_final: 0.5016 (pt0) REVERT: B 58 LYS cc_start: 0.8750 (mttp) cc_final: 0.8383 (mtmt) REVERT: B 235 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7400 (pp) REVERT: C 21 GLN cc_start: 0.8721 (tt0) cc_final: 0.8414 (tt0) REVERT: C 36 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7885 (mt) REVERT: C 58 LYS cc_start: 0.8792 (mttp) cc_final: 0.8539 (mtmt) REVERT: C 235 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7253 (pp) REVERT: C 412 ARG cc_start: 0.8535 (ptt90) cc_final: 0.8298 (ptt90) REVERT: C 453 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8002 (tt) REVERT: C 492 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8112 (mtpp) REVERT: C 510 GLU cc_start: 0.6419 (tp30) cc_final: 0.5064 (pt0) REVERT: D 21 GLN cc_start: 0.8776 (tt0) cc_final: 0.8478 (tt0) REVERT: D 36 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8034 (pp) REVERT: D 58 LYS cc_start: 0.8762 (mttp) cc_final: 0.8422 (mtmt) REVERT: D 235 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7357 (pp) REVERT: D 441 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: D 453 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7948 (tt) REVERT: D 491 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: D 510 GLU cc_start: 0.6201 (tp30) cc_final: 0.5009 (pt0) REVERT: E 58 LYS cc_start: 0.8795 (mttp) cc_final: 0.8534 (mtmt) REVERT: E 235 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7327 (pp) REVERT: E 492 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8114 (mtpt) REVERT: E 510 GLU cc_start: 0.6296 (tp30) cc_final: 0.4986 (pt0) REVERT: F 36 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7992 (pp) REVERT: F 58 LYS cc_start: 0.8843 (mttp) cc_final: 0.8522 (mtmt) REVERT: F 235 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7354 (pp) REVERT: F 453 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7883 (tt) REVERT: F 492 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8097 (mtpt) REVERT: F 510 GLU cc_start: 0.6218 (tp30) cc_final: 0.5021 (pt0) REVERT: G 58 LYS cc_start: 0.8813 (mttp) cc_final: 0.8553 (mtmt) REVERT: G 235 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7273 (pp) REVERT: G 453 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7887 (tt) REVERT: G 492 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8077 (mtpt) REVERT: G 510 GLU cc_start: 0.6308 (tp30) cc_final: 0.4964 (pt0) REVERT: H 50 ASP cc_start: 0.8219 (t70) cc_final: 0.7922 (t0) REVERT: H 58 LYS cc_start: 0.8779 (mttp) cc_final: 0.8458 (mtmt) REVERT: H 235 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7431 (pp) REVERT: H 453 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7767 (tt) REVERT: H 492 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8129 (mtpt) REVERT: H 510 GLU cc_start: 0.6253 (tp30) cc_final: 0.5095 (pt0) outliers start: 108 outliers final: 64 residues processed: 355 average time/residue: 1.2764 time to fit residues: 522.0503 Evaluate side-chains 367 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 277 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 492 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 208 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 264 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 334 GLN B 303 ASN B 334 GLN C 265 GLN C 303 ASN C 334 GLN D 303 ASN E 334 GLN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23096 Z= 0.240 Angle : 0.495 7.709 31208 Z= 0.253 Chirality : 0.043 0.143 3592 Planarity : 0.004 0.034 3976 Dihedral : 5.249 50.998 3292 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.53 % Allowed : 15.69 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.57 (0.15), residues: 2960 helix: 0.01 (0.15), residues: 1152 sheet: -0.82 (0.25), residues: 360 loop : -0.44 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 93 PHE 0.010 0.001 PHE F 401 TYR 0.010 0.001 TYR C 348 ARG 0.002 0.000 ARG E 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 276 time to evaluate : 2.700 Fit side-chains REVERT: A 36 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 58 LYS cc_start: 0.8751 (mttp) cc_final: 0.8474 (mtmt) REVERT: A 235 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 441 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6735 (mp10) REVERT: A 453 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7994 (tt) REVERT: B 58 LYS cc_start: 0.8740 (mttp) cc_final: 0.8378 (mtmt) REVERT: B 235 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7431 (pp) REVERT: C 21 GLN cc_start: 0.8760 (tt0) cc_final: 0.8459 (tt0) REVERT: C 36 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8152 (pp) REVERT: C 58 LYS cc_start: 0.8807 (mttp) cc_final: 0.8551 (mtmt) REVERT: C 235 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7279 (pp) REVERT: C 453 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8009 (tt) REVERT: C 492 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8100 (mtpp) REVERT: D 21 GLN cc_start: 0.8765 (tt0) cc_final: 0.8470 (tt0) REVERT: D 36 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8081 (pp) REVERT: D 58 LYS cc_start: 0.8791 (mttp) cc_final: 0.8457 (mtmt) REVERT: D 235 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7348 (pp) REVERT: D 441 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.6800 (mp10) REVERT: D 453 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7979 (tt) REVERT: D 491 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: D 510 GLU cc_start: 0.6233 (tp30) cc_final: 0.5028 (tp30) REVERT: D 512 ARG cc_start: 0.5367 (mmt180) cc_final: 0.5156 (mmt90) REVERT: E 36 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8094 (pp) REVERT: E 58 LYS cc_start: 0.8799 (mttp) cc_final: 0.8535 (mtmt) REVERT: E 235 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7328 (pp) REVERT: E 492 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8135 (mtpt) REVERT: E 510 GLU cc_start: 0.6325 (tp30) cc_final: 0.4992 (pt0) REVERT: F 36 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8040 (pp) REVERT: F 58 LYS cc_start: 0.8858 (mttp) cc_final: 0.8537 (mtmt) REVERT: F 235 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7320 (pp) REVERT: F 453 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7920 (tt) REVERT: F 492 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8140 (mtpp) REVERT: G 58 LYS cc_start: 0.8808 (mttp) cc_final: 0.8549 (mtmt) REVERT: G 235 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7282 (pp) REVERT: G 399 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7995 (mm-30) REVERT: G 453 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7879 (tt) REVERT: G 492 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8040 (mtpt) REVERT: G 510 GLU cc_start: 0.6344 (tp30) cc_final: 0.4992 (pt0) REVERT: H 50 ASP cc_start: 0.8227 (t70) cc_final: 0.7928 (t0) REVERT: H 58 LYS cc_start: 0.8808 (mttp) cc_final: 0.8494 (mtmt) REVERT: H 235 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7435 (pp) REVERT: H 453 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7808 (tt) REVERT: H 492 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8055 (mtpt) REVERT: H 510 GLU cc_start: 0.6289 (tp30) cc_final: 0.5101 (pt0) outliers start: 108 outliers final: 67 residues processed: 345 average time/residue: 1.2835 time to fit residues: 509.2385 Evaluate side-chains 367 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 273 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 492 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.9990 chunk 281 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 303 ASN B 334 GLN C 265 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN E 334 GLN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23096 Z= 0.220 Angle : 0.491 7.695 31208 Z= 0.250 Chirality : 0.043 0.143 3592 Planarity : 0.004 0.034 3976 Dihedral : 5.146 51.487 3292 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.36 % Allowed : 16.07 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.49 (0.15), residues: 2960 helix: 0.06 (0.15), residues: 1152 sheet: -0.81 (0.25), residues: 360 loop : -0.37 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 93 PHE 0.010 0.001 PHE F 401 TYR 0.010 0.001 TYR E 348 ARG 0.002 0.000 ARG C 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 281 time to evaluate : 2.551 Fit side-chains REVERT: A 36 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7965 (pp) REVERT: A 58 LYS cc_start: 0.8748 (mttp) cc_final: 0.8465 (mtmt) REVERT: A 235 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7260 (pp) REVERT: A 441 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: A 453 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7975 (tt) REVERT: A 510 GLU cc_start: 0.6346 (tp30) cc_final: 0.5012 (pt0) REVERT: B 36 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8015 (pp) REVERT: B 58 LYS cc_start: 0.8759 (mttp) cc_final: 0.8390 (mtmt) REVERT: B 235 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7445 (pp) REVERT: B 453 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7944 (tt) REVERT: C 21 GLN cc_start: 0.8702 (tt0) cc_final: 0.8399 (tt0) REVERT: C 36 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7899 (mt) REVERT: C 58 LYS cc_start: 0.8789 (mttp) cc_final: 0.8528 (mtmt) REVERT: C 235 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7263 (pp) REVERT: C 453 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7998 (tt) REVERT: C 492 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8096 (mtpt) REVERT: C 510 GLU cc_start: 0.6424 (tp30) cc_final: 0.5062 (pt0) REVERT: D 21 GLN cc_start: 0.8761 (tt0) cc_final: 0.8466 (tt0) REVERT: D 36 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8056 (pp) REVERT: D 58 LYS cc_start: 0.8779 (mttp) cc_final: 0.8454 (mtmt) REVERT: D 235 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7316 (pp) REVERT: D 441 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: D 453 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7959 (tt) REVERT: D 491 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: E 36 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (pp) REVERT: E 58 LYS cc_start: 0.8800 (mttp) cc_final: 0.8538 (mtmt) REVERT: E 235 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7316 (pp) REVERT: E 492 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8138 (mtpt) REVERT: E 510 GLU cc_start: 0.6313 (tp30) cc_final: 0.4991 (pt0) REVERT: F 36 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7988 (pp) REVERT: F 58 LYS cc_start: 0.8855 (mttp) cc_final: 0.8540 (mtmt) REVERT: F 235 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7268 (pp) REVERT: F 399 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7901 (mm-30) REVERT: F 453 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7904 (tt) REVERT: F 492 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8095 (mtpp) REVERT: G 36 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7963 (pp) REVERT: G 58 LYS cc_start: 0.8810 (mttp) cc_final: 0.8555 (mtmt) REVERT: G 235 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7253 (pp) REVERT: G 453 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7875 (tt) REVERT: G 492 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8053 (mtpt) REVERT: H 21 GLN cc_start: 0.8748 (tt0) cc_final: 0.8429 (tt0) REVERT: H 58 LYS cc_start: 0.8802 (mttp) cc_final: 0.8491 (mtmt) REVERT: H 235 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7417 (pp) REVERT: H 453 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7761 (tt) REVERT: H 492 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8096 (mtpp) REVERT: H 510 GLU cc_start: 0.6273 (tp30) cc_final: 0.5102 (pt0) outliers start: 104 outliers final: 66 residues processed: 347 average time/residue: 1.2803 time to fit residues: 513.4493 Evaluate side-chains 369 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 273 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 492 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 241 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 303 ASN B 334 GLN C 265 GLN C 303 ASN C 334 GLN D 303 ASN E 334 GLN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.099632 restraints weight = 25705.873| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.91 r_work: 0.2962 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23096 Z= 0.199 Angle : 0.485 7.471 31208 Z= 0.246 Chirality : 0.042 0.142 3592 Planarity : 0.003 0.034 3976 Dihedral : 5.041 50.439 3292 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.28 % Allowed : 16.32 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.41 (0.15), residues: 2960 helix: 0.14 (0.15), residues: 1152 sheet: -0.80 (0.25), residues: 360 loop : -0.34 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 92 PHE 0.009 0.001 PHE G 401 TYR 0.010 0.001 TYR E 459 ARG 0.002 0.000 ARG G 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8652.82 seconds wall clock time: 154 minutes 29.80 seconds (9269.80 seconds total)