Starting phenix.real_space_refine on Sun Feb 18 22:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8e_20687/02_2024/6u8e_20687_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8e_20687/02_2024/6u8e_20687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8e_20687/02_2024/6u8e_20687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8e_20687/02_2024/6u8e_20687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8e_20687/02_2024/6u8e_20687_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8e_20687/02_2024/6u8e_20687_updated.pdb" } resolution = 3.03 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= 0.049 sd= 2.559 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 24 5.49 5 S 144 5.16 5 C 14440 2.51 5 N 3912 2.21 5 O 4464 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22984 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "C" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "D" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "E" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "F" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "G" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "H" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 11.47, per 1000 atoms: 0.50 Number of scatterers: 22984 At special positions: 0 Unit cell: (122.85, 122.85, 120.75, 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 24 15.00 O 4464 8.00 N 3912 7.00 C 14440 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.36 Conformation dependent library (CDL) restraints added in 4.4 seconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 32 sheets defined 34.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 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 76 through 84 removed outlier: 3.780A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.555A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 264 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 4.060A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.518A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.818A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 4.298A 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 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' 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 501 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 76 through 84 removed outlier: 3.779A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.554A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 264 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 265 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 4.059A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.519A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.817A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.298A 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 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' 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 501 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 76 through 84 removed outlier: 3.779A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.554A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA C 264 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 265 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 4.059A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.518A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 356 removed outlier: 3.817A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.298A 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 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' 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 501 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 76 through 84 removed outlier: 3.779A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.554A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 264 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 265 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 4.060A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 removed outlier: 3.518A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 356 removed outlier: 3.818A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.298A 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 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' 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 501 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 76 through 84 removed outlier: 3.779A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.554A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA E 264 " --> pdb=" O ASP E 261 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 265 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 4.060A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 removed outlier: 3.518A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 356 removed outlier: 3.817A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.298A 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 453 through 455 No H-bonds generated for 'chain 'E' and resid 453 through 455' 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 501 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 76 through 84 removed outlier: 3.779A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 109 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.555A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 264 " --> pdb=" O ASP F 261 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN F 265 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 4.059A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 removed outlier: 3.517A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 356 removed outlier: 3.818A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.298A 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 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' 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 501 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 76 through 84 removed outlier: 3.779A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 109 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.555A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA G 264 " --> pdb=" O ASP G 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN G 265 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 4.059A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 removed outlier: 3.518A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 356 removed outlier: 3.817A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.298A 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 453 through 455 No H-bonds generated for 'chain 'G' and resid 453 through 455' 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 501 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 76 through 84 removed outlier: 3.779A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 109 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.555A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA H 264 " --> pdb=" O ASP H 261 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN H 265 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 4.059A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 removed outlier: 3.518A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 356 removed outlier: 3.818A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.298A 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 453 through 455 No H-bonds generated for 'chain 'H' and resid 453 through 455' 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 501 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: 5.743A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.610A 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: 6.515A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.034A 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 401 through 403 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: 5.744A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.609A 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: 6.515A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.034A 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 401 through 403 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: 5.743A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.610A 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: 6.515A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.034A 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 401 through 403 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: 5.744A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.609A 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: 6.515A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.035A 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 401 through 403 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: 5.743A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.610A 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: 6.515A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.035A 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 401 through 403 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: 5.743A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 3.610A 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: 6.515A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.035A 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 401 through 403 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: 5.744A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.609A 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: 6.515A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.034A 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 401 through 403 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: 5.743A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.611A 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: 6.515A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.035A 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 401 through 403 624 hydrogen bonds defined for protein. 1680 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: 7.41 Time building geometry restraints manager: 9.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3832 1.30 - 1.43: 5675 1.43 - 1.55: 13573 1.55 - 1.68: 56 1.68 - 1.81: 240 Bond restraints: 23376 Sorted by residual: bond pdb=" C3D NAD F 602 " pdb=" C4D NAD F 602 " ideal model delta sigma weight residual 1.531 1.298 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.298 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C3D NAD E 602 " pdb=" C4D NAD E 602 " ideal model delta sigma weight residual 1.531 1.298 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C3D NAD A 602 " pdb=" C4D NAD A 602 " ideal model delta sigma weight residual 1.531 1.298 0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C3D NAD B 602 " pdb=" C4D NAD B 602 " ideal model delta sigma weight residual 1.531 1.299 0.232 2.00e-02 2.50e+03 1.35e+02 ... (remaining 23371 not shown) Histogram of bond angle deviations from ideal: 98.14 - 106.42: 600 106.42 - 114.70: 14120 114.70 - 122.98: 15520 122.98 - 131.25: 1342 131.25 - 139.53: 58 Bond angle restraints: 31640 Sorted by residual: angle pdb=" N1A NAD G 602 " pdb=" C6A NAD G 602 " pdb=" N6A NAD G 602 " ideal model delta sigma weight residual 119.35 102.72 16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" N1A NAD C 602 " pdb=" C6A NAD C 602 " pdb=" N6A NAD C 602 " ideal model delta sigma weight residual 119.35 102.73 16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" N1A NAD B 602 " pdb=" C6A NAD B 602 " pdb=" N6A NAD B 602 " ideal model delta sigma weight residual 119.35 102.75 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" N1A NAD E 602 " pdb=" C6A NAD E 602 " pdb=" N6A NAD E 602 " ideal model delta sigma weight residual 119.35 102.76 16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" N1A NAD H 602 " pdb=" C6A NAD H 602 " pdb=" N6A NAD H 602 " ideal model delta sigma weight residual 119.35 102.77 16.58 3.00e+00 1.11e-01 3.05e+01 ... (remaining 31635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 13604 28.40 - 56.81: 568 56.81 - 85.21: 24 85.21 - 113.62: 0 113.62 - 142.02: 4 Dihedral angle restraints: 14200 sinusoidal: 5728 harmonic: 8472 Sorted by residual: 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 -26.05 -142.02 1 2.00e+01 2.50e-03 4.29e+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 -26.07 -142.00 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" C5' IMP D 601 " pdb=" O5' IMP D 601 " pdb=" P IMP D 601 " pdb=" O2P IMP D 601 " ideal model delta sinusoidal sigma weight residual -168.07 -26.07 -142.00 1 2.00e+01 2.50e-03 4.29e+01 ... (remaining 14197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2651 0.065 - 0.130: 856 0.130 - 0.195: 109 0.195 - 0.260: 16 0.260 - 0.326: 16 Chirality restraints: 3648 Sorted by residual: chirality pdb=" C3D NAD E 602 " pdb=" C2D NAD E 602 " pdb=" C4D NAD E 602 " pdb=" O3D NAD E 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3D NAD A 602 " pdb=" C2D NAD A 602 " pdb=" C4D NAD A 602 " pdb=" O3D NAD A 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C3D NAD G 602 " pdb=" C2D NAD G 602 " pdb=" C4D NAD G 602 " pdb=" O3D NAD G 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 3645 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 13 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C VAL E 13 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL E 13 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO E 14 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 13 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C VAL D 13 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL D 13 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO D 14 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 13 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C VAL C 13 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL C 13 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO C 14 " 0.016 2.00e-02 2.50e+03 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6925 2.80 - 3.32: 20992 3.32 - 3.85: 39472 3.85 - 4.37: 47508 4.37 - 4.90: 79398 Nonbonded interactions: 194295 Sorted by model distance: nonbonded pdb=" OD1 ASP G 261 " pdb=" OH TYR G 294 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASP F 261 " pdb=" OH TYR F 294 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASP H 261 " pdb=" OH TYR H 294 " model vdw 2.275 2.440 nonbonded pdb=" OD1 ASP E 261 " pdb=" OH TYR E 294 " model vdw 2.275 2.440 nonbonded pdb=" OD1 ASP C 261 " pdb=" OH TYR C 294 " model vdw 2.275 2.440 ... (remaining 194290 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: 2.790 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: 7.710 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 59.610 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.014 0.233 23376 Z= 0.925 Angle : 1.251 16.626 31640 Z= 0.626 Chirality : 0.064 0.326 3648 Planarity : 0.006 0.046 3976 Dihedral : 13.483 142.020 8824 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.02 % Allowed : 6.19 % Favored : 91.79 % 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: -3.92 (0.12), residues: 2952 helix: -3.05 (0.10), residues: 1080 sheet: -3.20 (0.20), residues: 496 loop : -1.79 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 92 PHE 0.021 0.003 PHE A 401 TYR 0.017 0.003 TYR F 484 ARG 0.008 0.002 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 779 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6630 (mt) REVERT: A 269 ASP cc_start: 0.8427 (m-30) cc_final: 0.8202 (m-30) REVERT: A 329 SER cc_start: 0.9362 (p) cc_final: 0.9030 (p) REVERT: A 399 GLU cc_start: 0.8352 (pm20) cc_final: 0.8021 (pm20) REVERT: A 417 LEU cc_start: 0.8685 (pt) cc_final: 0.8482 (pp) REVERT: A 482 MET cc_start: 0.8835 (mtp) cc_final: 0.8537 (mtm) REVERT: A 483 MET cc_start: 0.9303 (tmm) cc_final: 0.8318 (tmm) REVERT: A 487 GLU cc_start: 0.8832 (tt0) cc_final: 0.8473 (tt0) REVERT: A 512 ARG cc_start: 0.8654 (mtp-110) cc_final: 0.8334 (ttp-110) REVERT: B 16 ASP cc_start: 0.8699 (t0) cc_final: 0.8431 (t0) REVERT: B 28 ASP cc_start: 0.8693 (m-30) cc_final: 0.8386 (m-30) REVERT: B 84 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6614 (mt) REVERT: B 243 GLN cc_start: 0.8219 (mt0) cc_final: 0.7702 (mt0) REVERT: B 254 GLU cc_start: 0.8938 (tp30) cc_final: 0.8673 (tp30) REVERT: B 269 ASP cc_start: 0.8524 (m-30) cc_final: 0.8109 (m-30) REVERT: B 329 SER cc_start: 0.9409 (p) cc_final: 0.9081 (p) REVERT: B 399 GLU cc_start: 0.8422 (pm20) cc_final: 0.8083 (pm20) REVERT: B 417 LEU cc_start: 0.8699 (pt) cc_final: 0.8470 (pt) REVERT: B 482 MET cc_start: 0.8727 (mtp) cc_final: 0.8438 (mtm) REVERT: B 483 MET cc_start: 0.9439 (tmm) cc_final: 0.8409 (tmm) REVERT: B 487 GLU cc_start: 0.8768 (tt0) cc_final: 0.8393 (tt0) REVERT: C 28 ASP cc_start: 0.8708 (m-30) cc_final: 0.8504 (m-30) REVERT: C 62 LYS cc_start: 0.8510 (mmtp) cc_final: 0.8214 (mmtm) REVERT: C 84 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6798 (mt) REVERT: C 269 ASP cc_start: 0.8490 (m-30) cc_final: 0.8058 (m-30) REVERT: C 329 SER cc_start: 0.9366 (p) cc_final: 0.9081 (p) REVERT: C 399 GLU cc_start: 0.8319 (pm20) cc_final: 0.8023 (pm20) REVERT: C 482 MET cc_start: 0.8865 (mtp) cc_final: 0.8614 (mtm) REVERT: C 487 GLU cc_start: 0.8819 (tt0) cc_final: 0.8495 (tt0) REVERT: C 512 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8386 (ttp-110) REVERT: D 28 ASP cc_start: 0.8726 (m-30) cc_final: 0.8495 (m-30) REVERT: D 102 ASN cc_start: 0.9046 (t0) cc_final: 0.8741 (t0) REVERT: D 108 LYS cc_start: 0.8929 (tttt) cc_final: 0.8691 (tptt) REVERT: D 269 ASP cc_start: 0.8520 (m-30) cc_final: 0.8122 (m-30) REVERT: D 329 SER cc_start: 0.9364 (p) cc_final: 0.9056 (p) REVERT: D 399 GLU cc_start: 0.8355 (pm20) cc_final: 0.8054 (pm20) REVERT: D 482 MET cc_start: 0.8815 (mtp) cc_final: 0.8551 (mtm) REVERT: D 487 GLU cc_start: 0.8792 (tt0) cc_final: 0.8463 (tt0) REVERT: E 16 ASP cc_start: 0.8555 (t0) cc_final: 0.8250 (t0) REVERT: E 28 ASP cc_start: 0.8685 (m-30) cc_final: 0.8431 (m-30) REVERT: E 62 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8275 (mmtp) REVERT: E 84 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6713 (mt) REVERT: E 269 ASP cc_start: 0.8428 (m-30) cc_final: 0.8005 (m-30) REVERT: E 329 SER cc_start: 0.9354 (p) cc_final: 0.9030 (p) REVERT: E 399 GLU cc_start: 0.8327 (pm20) cc_final: 0.8007 (pm20) REVERT: E 417 LEU cc_start: 0.8635 (pt) cc_final: 0.8415 (pp) REVERT: E 482 MET cc_start: 0.8839 (mtp) cc_final: 0.8574 (mtm) REVERT: E 483 MET cc_start: 0.9435 (tmm) cc_final: 0.8387 (tmm) REVERT: E 487 GLU cc_start: 0.8830 (tt0) cc_final: 0.8489 (tt0) REVERT: E 512 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8455 (ttp-110) REVERT: F 28 ASP cc_start: 0.8700 (m-30) cc_final: 0.8433 (m-30) REVERT: F 84 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6485 (mt) REVERT: F 102 ASN cc_start: 0.9010 (t0) cc_final: 0.8685 (t0) REVERT: F 108 LYS cc_start: 0.8911 (tttt) cc_final: 0.8673 (tptt) REVERT: F 269 ASP cc_start: 0.8530 (m-30) cc_final: 0.8121 (m-30) REVERT: F 329 SER cc_start: 0.9380 (p) cc_final: 0.9046 (p) REVERT: F 399 GLU cc_start: 0.8394 (pm20) cc_final: 0.8050 (pm20) REVERT: F 417 LEU cc_start: 0.8625 (pt) cc_final: 0.8424 (pt) REVERT: F 482 MET cc_start: 0.8749 (mtp) cc_final: 0.8464 (mtm) REVERT: F 483 MET cc_start: 0.9435 (tmm) cc_final: 0.8402 (tmm) REVERT: F 487 GLU cc_start: 0.8800 (tt0) cc_final: 0.8455 (tt0) REVERT: G 16 ASP cc_start: 0.8594 (t0) cc_final: 0.8296 (t0) REVERT: G 28 ASP cc_start: 0.8700 (m-30) cc_final: 0.8462 (m-30) REVERT: G 84 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6624 (mt) REVERT: G 254 GLU cc_start: 0.8868 (tp30) cc_final: 0.8660 (tp30) REVERT: G 269 ASP cc_start: 0.8460 (m-30) cc_final: 0.8033 (m-30) REVERT: G 329 SER cc_start: 0.9346 (p) cc_final: 0.9010 (p) REVERT: G 399 GLU cc_start: 0.8350 (pm20) cc_final: 0.8000 (pm20) REVERT: G 482 MET cc_start: 0.8877 (mtp) cc_final: 0.8577 (mtm) REVERT: G 487 GLU cc_start: 0.8838 (tt0) cc_final: 0.8490 (tt0) REVERT: G 512 ARG cc_start: 0.8635 (mtp-110) cc_final: 0.8382 (ttp-110) REVERT: H 28 ASP cc_start: 0.8703 (m-30) cc_final: 0.8421 (m-30) REVERT: H 78 MET cc_start: 0.9092 (tpt) cc_final: 0.8862 (tpp) REVERT: H 105 ARG cc_start: 0.8595 (tmm160) cc_final: 0.8392 (ttp80) REVERT: H 329 SER cc_start: 0.9398 (p) cc_final: 0.9082 (p) REVERT: H 399 GLU cc_start: 0.8349 (pm20) cc_final: 0.8057 (pm20) REVERT: H 482 MET cc_start: 0.8776 (mtp) cc_final: 0.8513 (mtm) REVERT: H 483 MET cc_start: 0.9416 (tmm) cc_final: 0.8446 (tmm) REVERT: H 487 GLU cc_start: 0.8792 (tt0) cc_final: 0.8435 (tt0) outliers start: 48 outliers final: 6 residues processed: 814 average time/residue: 0.3510 time to fit residues: 441.0105 Evaluate side-chains 539 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 527 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 84 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.9980 chunk 224 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 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 25 ASN A 48 GLN A 243 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 48 GLN C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 243 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 243 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 243 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 243 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN H 243 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23376 Z= 0.211 Angle : 0.532 6.439 31640 Z= 0.279 Chirality : 0.042 0.159 3648 Planarity : 0.004 0.038 3976 Dihedral : 9.431 66.127 3730 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.49 % Allowed : 10.23 % Favored : 86.28 % 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: -2.45 (0.14), residues: 2952 helix: -1.30 (0.14), residues: 1080 sheet: -2.80 (0.21), residues: 456 loop : -1.33 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 92 PHE 0.012 0.001 PHE D 401 TYR 0.022 0.002 TYR G 12 ARG 0.005 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 576 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6623 (mt) REVERT: A 269 ASP cc_start: 0.8506 (m-30) cc_final: 0.8083 (m-30) REVERT: A 329 SER cc_start: 0.9504 (p) cc_final: 0.9210 (p) REVERT: A 399 GLU cc_start: 0.8264 (pm20) cc_final: 0.7912 (pm20) REVERT: A 487 GLU cc_start: 0.8906 (tt0) cc_final: 0.8617 (tt0) REVERT: A 512 ARG cc_start: 0.8673 (mtp-110) cc_final: 0.8442 (ttp-110) REVERT: B 16 ASP cc_start: 0.8803 (t0) cc_final: 0.8573 (t0) REVERT: B 28 ASP cc_start: 0.8643 (m-30) cc_final: 0.8370 (m-30) REVERT: B 84 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6642 (mt) REVERT: B 105 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8344 (ttp80) REVERT: B 269 ASP cc_start: 0.8402 (m-30) cc_final: 0.8150 (m-30) REVERT: B 277 GLN cc_start: 0.8635 (tp40) cc_final: 0.8286 (tp40) REVERT: B 329 SER cc_start: 0.9533 (p) cc_final: 0.9247 (p) REVERT: B 385 MET cc_start: 0.8588 (ttm) cc_final: 0.8256 (ttp) REVERT: B 399 GLU cc_start: 0.8270 (pm20) cc_final: 0.7904 (pm20) REVERT: B 487 GLU cc_start: 0.8810 (tt0) cc_final: 0.8549 (tt0) REVERT: C 28 ASP cc_start: 0.8735 (m-30) cc_final: 0.8484 (m-30) REVERT: C 62 LYS cc_start: 0.8535 (mmtp) cc_final: 0.8287 (mmtm) REVERT: C 84 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6758 (mt) REVERT: C 269 ASP cc_start: 0.8461 (m-30) cc_final: 0.8084 (m-30) REVERT: C 329 SER cc_start: 0.9491 (p) cc_final: 0.9216 (p) REVERT: C 399 GLU cc_start: 0.8275 (pm20) cc_final: 0.7943 (pm20) REVERT: C 482 MET cc_start: 0.8898 (mtp) cc_final: 0.8618 (mtm) REVERT: C 483 MET cc_start: 0.9380 (tmm) cc_final: 0.8317 (tmm) REVERT: C 487 GLU cc_start: 0.8811 (tt0) cc_final: 0.8483 (tt0) REVERT: C 512 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8366 (ttp-110) REVERT: D 16 ASP cc_start: 0.8866 (t0) cc_final: 0.8550 (t0) REVERT: D 269 ASP cc_start: 0.8541 (m-30) cc_final: 0.8072 (m-30) REVERT: D 329 SER cc_start: 0.9488 (p) cc_final: 0.9217 (p) REVERT: D 399 GLU cc_start: 0.8250 (pm20) cc_final: 0.7904 (pm20) REVERT: D 417 LEU cc_start: 0.8622 (pt) cc_final: 0.8397 (pt) REVERT: D 482 MET cc_start: 0.8802 (mtp) cc_final: 0.8509 (mtm) REVERT: D 487 GLU cc_start: 0.8783 (tt0) cc_final: 0.8448 (tt0) REVERT: E 16 ASP cc_start: 0.8703 (t0) cc_final: 0.8498 (t0) REVERT: E 28 ASP cc_start: 0.8702 (m-30) cc_final: 0.8335 (m-30) REVERT: E 62 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8084 (mmmt) REVERT: E 84 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6672 (mt) REVERT: E 269 ASP cc_start: 0.8413 (m-30) cc_final: 0.8042 (m-30) REVERT: E 329 SER cc_start: 0.9401 (p) cc_final: 0.9080 (p) REVERT: E 385 MET cc_start: 0.8492 (ttm) cc_final: 0.8138 (ttp) REVERT: E 399 GLU cc_start: 0.8238 (pm20) cc_final: 0.7904 (pm20) REVERT: E 407 ARG cc_start: 0.8670 (ttt180) cc_final: 0.8099 (ttt90) REVERT: E 487 GLU cc_start: 0.8856 (tt0) cc_final: 0.8600 (tt0) REVERT: E 512 ARG cc_start: 0.8652 (mtp-110) cc_final: 0.8449 (ttp-110) REVERT: F 28 ASP cc_start: 0.8710 (m-30) cc_final: 0.8326 (m-30) REVERT: F 84 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6625 (mt) REVERT: F 254 GLU cc_start: 0.8937 (tp30) cc_final: 0.8717 (tp30) REVERT: F 269 ASP cc_start: 0.8564 (m-30) cc_final: 0.8006 (m-30) REVERT: F 329 SER cc_start: 0.9428 (p) cc_final: 0.9113 (p) REVERT: F 385 MET cc_start: 0.8563 (ttm) cc_final: 0.8250 (ttp) REVERT: F 399 GLU cc_start: 0.8255 (pm20) cc_final: 0.7919 (pm20) REVERT: F 417 LEU cc_start: 0.8556 (pt) cc_final: 0.8343 (pt) REVERT: F 487 GLU cc_start: 0.8841 (tt0) cc_final: 0.8586 (tt0) REVERT: G 84 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6643 (mt) REVERT: G 254 GLU cc_start: 0.8817 (tp30) cc_final: 0.8551 (tp30) REVERT: G 269 ASP cc_start: 0.8438 (m-30) cc_final: 0.8063 (m-30) REVERT: G 277 GLN cc_start: 0.8618 (tp40) cc_final: 0.8336 (tp40) REVERT: G 329 SER cc_start: 0.9389 (p) cc_final: 0.9051 (p) REVERT: G 385 MET cc_start: 0.8543 (ttm) cc_final: 0.8209 (ttp) REVERT: G 399 GLU cc_start: 0.8262 (pm20) cc_final: 0.7889 (pm20) REVERT: G 482 MET cc_start: 0.8943 (mtp) cc_final: 0.8565 (mtm) REVERT: G 483 MET cc_start: 0.9361 (tmm) cc_final: 0.8376 (tmm) REVERT: G 487 GLU cc_start: 0.8859 (tt0) cc_final: 0.8462 (tt0) REVERT: G 512 ARG cc_start: 0.8682 (mtp-110) cc_final: 0.8390 (ttp-110) REVERT: H 16 ASP cc_start: 0.8808 (t0) cc_final: 0.8472 (t0) REVERT: H 28 ASP cc_start: 0.8681 (m-30) cc_final: 0.8262 (m-30) REVERT: H 254 GLU cc_start: 0.8995 (tp30) cc_final: 0.8779 (tp30) REVERT: H 277 GLN cc_start: 0.8574 (tp40) cc_final: 0.8242 (tp40) REVERT: H 329 SER cc_start: 0.9433 (p) cc_final: 0.9116 (p) REVERT: H 399 GLU cc_start: 0.8280 (pm20) cc_final: 0.7912 (pm20) REVERT: H 487 GLU cc_start: 0.8823 (tt0) cc_final: 0.8550 (tt0) outliers start: 83 outliers final: 18 residues processed: 613 average time/residue: 0.2979 time to fit residues: 296.1959 Evaluate side-chains 530 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 506 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 269 ASP 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: 0.3980 chunk 223 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 216 optimal weight: 3.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN A 498 GLN B 102 ASN B 253 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN F 102 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 253 HIS ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23376 Z= 0.253 Angle : 0.520 7.328 31640 Z= 0.266 Chirality : 0.043 0.172 3648 Planarity : 0.003 0.036 3976 Dihedral : 8.767 64.313 3724 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.87 % Allowed : 11.36 % Favored : 84.76 % 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: -1.70 (0.15), residues: 2952 helix: -0.40 (0.15), residues: 1080 sheet: -2.68 (0.20), residues: 456 loop : -1.03 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 92 PHE 0.011 0.001 PHE H 401 TYR 0.013 0.001 TYR F 12 ARG 0.004 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 544 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 254 GLU cc_start: 0.9039 (tp30) cc_final: 0.8749 (tp30) REVERT: A 269 ASP cc_start: 0.8284 (m-30) cc_final: 0.7916 (m-30) REVERT: A 329 SER cc_start: 0.9513 (p) cc_final: 0.9252 (p) REVERT: A 399 GLU cc_start: 0.8319 (pm20) cc_final: 0.7975 (pm20) REVERT: A 483 MET cc_start: 0.9369 (tmm) cc_final: 0.8330 (tmm) REVERT: A 487 GLU cc_start: 0.8893 (tt0) cc_final: 0.8641 (tt0) REVERT: A 512 ARG cc_start: 0.8611 (mtp-110) cc_final: 0.8231 (ttp-110) REVERT: B 16 ASP cc_start: 0.8780 (t0) cc_final: 0.8540 (t0) REVERT: B 28 ASP cc_start: 0.8685 (m-30) cc_final: 0.8358 (m-30) REVERT: B 75 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 84 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6592 (mt) REVERT: B 254 GLU cc_start: 0.8959 (tp30) cc_final: 0.8741 (tp30) REVERT: B 269 ASP cc_start: 0.8385 (m-30) cc_final: 0.8084 (m-30) REVERT: B 277 GLN cc_start: 0.8533 (tp40) cc_final: 0.8268 (tp40) REVERT: B 329 SER cc_start: 0.9555 (p) cc_final: 0.9307 (p) REVERT: B 385 MET cc_start: 0.8674 (ttm) cc_final: 0.8313 (ttp) REVERT: B 399 GLU cc_start: 0.8329 (pm20) cc_final: 0.7966 (pm20) REVERT: B 420 MET cc_start: 0.5369 (ttm) cc_final: 0.5159 (ttm) REVERT: B 483 MET cc_start: 0.9456 (tmm) cc_final: 0.8432 (tmm) REVERT: B 487 GLU cc_start: 0.8764 (tt0) cc_final: 0.8505 (tt0) REVERT: C 28 ASP cc_start: 0.8737 (m-30) cc_final: 0.8491 (m-30) REVERT: C 75 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7507 (mm-30) REVERT: C 80 ILE cc_start: 0.9506 (mt) cc_final: 0.9262 (mm) REVERT: C 84 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6722 (mt) REVERT: C 254 GLU cc_start: 0.9013 (tp30) cc_final: 0.8688 (tp30) REVERT: C 269 ASP cc_start: 0.8251 (m-30) cc_final: 0.7906 (m-30) REVERT: C 329 SER cc_start: 0.9527 (p) cc_final: 0.9298 (p) REVERT: C 399 GLU cc_start: 0.8313 (pm20) cc_final: 0.7996 (pm20) REVERT: C 482 MET cc_start: 0.8912 (mtp) cc_final: 0.8640 (mtm) REVERT: C 483 MET cc_start: 0.9384 (tmm) cc_final: 0.8422 (tmm) REVERT: C 487 GLU cc_start: 0.8868 (tt0) cc_final: 0.8560 (tt0) REVERT: C 512 ARG cc_start: 0.8636 (mtp-110) cc_final: 0.8288 (ttp-110) REVERT: D 16 ASP cc_start: 0.8866 (t0) cc_final: 0.8490 (t0) REVERT: D 28 ASP cc_start: 0.8553 (m-30) cc_final: 0.8265 (m-30) REVERT: D 75 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7666 (mm-30) REVERT: D 269 ASP cc_start: 0.8447 (m-30) cc_final: 0.8145 (m-30) REVERT: D 329 SER cc_start: 0.9513 (p) cc_final: 0.9268 (p) REVERT: D 399 GLU cc_start: 0.8297 (pm20) cc_final: 0.7955 (pm20) REVERT: D 417 LEU cc_start: 0.8657 (pt) cc_final: 0.8375 (pt) REVERT: D 482 MET cc_start: 0.8828 (mtp) cc_final: 0.8556 (mtm) REVERT: D 483 MET cc_start: 0.9379 (tmm) cc_final: 0.8432 (tmm) REVERT: D 487 GLU cc_start: 0.8850 (tt0) cc_final: 0.8540 (tt0) REVERT: D 512 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8577 (ttp-110) REVERT: E 16 ASP cc_start: 0.8691 (t0) cc_final: 0.8450 (t0) REVERT: E 28 ASP cc_start: 0.8705 (m-30) cc_final: 0.8385 (m-30) REVERT: E 75 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7601 (mm-30) REVERT: E 84 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6599 (mt) REVERT: E 98 GLU cc_start: 0.8763 (pm20) cc_final: 0.8415 (mp0) REVERT: E 103 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8227 (mm-30) REVERT: E 269 ASP cc_start: 0.8259 (m-30) cc_final: 0.7930 (m-30) REVERT: E 329 SER cc_start: 0.9414 (p) cc_final: 0.9107 (p) REVERT: E 399 GLU cc_start: 0.8301 (pm20) cc_final: 0.7965 (pm20) REVERT: E 407 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8144 (ttt-90) REVERT: E 483 MET cc_start: 0.9454 (tmm) cc_final: 0.8420 (tmm) REVERT: E 487 GLU cc_start: 0.8884 (tt0) cc_final: 0.8615 (tt0) REVERT: E 512 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.8455 (ttp-110) REVERT: F 16 ASP cc_start: 0.8716 (t0) cc_final: 0.8431 (t0) REVERT: F 28 ASP cc_start: 0.8740 (m-30) cc_final: 0.8501 (m-30) REVERT: F 75 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7526 (mm-30) REVERT: F 80 ILE cc_start: 0.9312 (pt) cc_final: 0.9098 (mm) REVERT: F 84 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6525 (mt) REVERT: F 254 GLU cc_start: 0.8941 (tp30) cc_final: 0.8721 (tp30) REVERT: F 269 ASP cc_start: 0.8298 (m-30) cc_final: 0.7993 (m-30) REVERT: F 329 SER cc_start: 0.9437 (p) cc_final: 0.9159 (p) REVERT: F 385 MET cc_start: 0.8699 (ttm) cc_final: 0.8362 (ttp) REVERT: F 399 GLU cc_start: 0.8307 (pm20) cc_final: 0.7944 (pm20) REVERT: F 417 LEU cc_start: 0.8552 (pt) cc_final: 0.8305 (pt) REVERT: F 483 MET cc_start: 0.9444 (tmm) cc_final: 0.8525 (tmm) REVERT: F 487 GLU cc_start: 0.8875 (tt0) cc_final: 0.8609 (tt0) REVERT: G 16 ASP cc_start: 0.8713 (t0) cc_final: 0.8296 (t0) REVERT: G 75 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7490 (mm-30) REVERT: G 84 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6591 (mt) REVERT: G 105 ARG cc_start: 0.8715 (tmm160) cc_final: 0.8454 (ttp80) REVERT: G 254 GLU cc_start: 0.8842 (tp30) cc_final: 0.8411 (tp30) REVERT: G 269 ASP cc_start: 0.8272 (m-30) cc_final: 0.7883 (m-30) REVERT: G 329 SER cc_start: 0.9372 (p) cc_final: 0.9058 (p) REVERT: G 385 MET cc_start: 0.8645 (ttm) cc_final: 0.8323 (ttp) REVERT: G 399 GLU cc_start: 0.8311 (pm20) cc_final: 0.7957 (pm20) REVERT: G 483 MET cc_start: 0.9379 (tmm) cc_final: 0.8414 (tmm) REVERT: G 487 GLU cc_start: 0.8879 (tt0) cc_final: 0.8630 (tt0) REVERT: G 512 ARG cc_start: 0.8647 (mtp-110) cc_final: 0.8291 (ttp-110) REVERT: H 75 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7665 (mm-30) REVERT: H 254 GLU cc_start: 0.8971 (tp30) cc_final: 0.8706 (tp30) REVERT: H 277 GLN cc_start: 0.8485 (tp40) cc_final: 0.8243 (tp40) REVERT: H 329 SER cc_start: 0.9438 (p) cc_final: 0.9149 (p) REVERT: H 399 GLU cc_start: 0.8306 (pm20) cc_final: 0.7966 (pm20) REVERT: H 483 MET cc_start: 0.9445 (tmm) cc_final: 0.8472 (tmm) REVERT: H 487 GLU cc_start: 0.8852 (tt0) cc_final: 0.8585 (tt0) REVERT: H 512 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8386 (ttp80) outliers start: 92 outliers final: 43 residues processed: 594 average time/residue: 0.3154 time to fit residues: 303.8583 Evaluate side-chains 553 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 504 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 0.0370 chunk 202 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 256 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN C 498 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN F 102 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN F 498 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23376 Z= 0.173 Angle : 0.471 6.388 31640 Z= 0.241 Chirality : 0.041 0.138 3648 Planarity : 0.003 0.036 3976 Dihedral : 8.355 63.966 3724 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.75 % Allowed : 12.75 % Favored : 83.50 % 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: -1.20 (0.15), residues: 2952 helix: 0.18 (0.16), residues: 1080 sheet: -2.55 (0.20), residues: 456 loop : -0.84 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.011 0.001 PHE E 401 TYR 0.009 0.001 TYR C 348 ARG 0.003 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 542 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8745 (t0) cc_final: 0.8434 (t0) REVERT: A 75 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7834 (mm-30) REVERT: A 269 ASP cc_start: 0.8107 (m-30) cc_final: 0.7839 (m-30) REVERT: A 329 SER cc_start: 0.9505 (p) cc_final: 0.9243 (p) REVERT: A 399 GLU cc_start: 0.8311 (pm20) cc_final: 0.8032 (pm20) REVERT: A 483 MET cc_start: 0.9368 (tmm) cc_final: 0.8356 (tmm) REVERT: A 487 GLU cc_start: 0.8876 (tt0) cc_final: 0.8634 (tt0) REVERT: A 512 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8180 (ttp-110) REVERT: B 16 ASP cc_start: 0.8756 (t0) cc_final: 0.8510 (t0) REVERT: B 28 ASP cc_start: 0.8665 (m-30) cc_final: 0.8339 (m-30) REVERT: B 75 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 102 ASN cc_start: 0.9047 (t0) cc_final: 0.8759 (t0) REVERT: B 105 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8258 (ttp80) REVERT: B 254 GLU cc_start: 0.8926 (tp30) cc_final: 0.8721 (tp30) REVERT: B 385 MET cc_start: 0.8617 (ttm) cc_final: 0.8252 (ttp) REVERT: B 399 GLU cc_start: 0.8298 (pm20) cc_final: 0.8000 (pm20) REVERT: B 410 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8275 (ttmm) REVERT: B 483 MET cc_start: 0.9463 (tmm) cc_final: 0.8483 (tmm) REVERT: C 16 ASP cc_start: 0.8716 (t0) cc_final: 0.8461 (t0) REVERT: C 28 ASP cc_start: 0.8700 (m-30) cc_final: 0.8467 (m-30) REVERT: C 75 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7798 (mm-30) REVERT: C 84 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6607 (mt) REVERT: C 254 GLU cc_start: 0.8940 (tp30) cc_final: 0.8612 (tp30) REVERT: C 269 ASP cc_start: 0.8106 (m-30) cc_final: 0.7886 (m-30) REVERT: C 399 GLU cc_start: 0.8322 (pm20) cc_final: 0.8030 (pm20) REVERT: C 487 GLU cc_start: 0.8877 (tt0) cc_final: 0.8637 (tt0) REVERT: C 512 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8297 (ttp-110) REVERT: D 16 ASP cc_start: 0.8865 (t0) cc_final: 0.8479 (t0) REVERT: D 28 ASP cc_start: 0.8506 (m-30) cc_final: 0.8243 (m-30) REVERT: D 75 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8056 (mm-30) REVERT: D 84 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6156 (mt) REVERT: D 399 GLU cc_start: 0.8276 (pm20) cc_final: 0.7989 (pm20) REVERT: D 410 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8314 (ttmm) REVERT: D 417 LEU cc_start: 0.8601 (pt) cc_final: 0.8388 (pt) REVERT: D 487 GLU cc_start: 0.8852 (tt0) cc_final: 0.8583 (tt0) REVERT: D 512 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8589 (ttp-110) REVERT: E 16 ASP cc_start: 0.8675 (t0) cc_final: 0.8470 (t0) REVERT: E 28 ASP cc_start: 0.8674 (m-30) cc_final: 0.8403 (m-30) REVERT: E 75 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7572 (mm-30) REVERT: E 98 GLU cc_start: 0.8732 (pm20) cc_final: 0.8406 (mp0) REVERT: E 256 ASP cc_start: 0.8935 (m-30) cc_final: 0.8681 (t0) REVERT: E 269 ASP cc_start: 0.8125 (m-30) cc_final: 0.7844 (m-30) REVERT: E 329 SER cc_start: 0.9446 (p) cc_final: 0.9177 (p) REVERT: E 393 THR cc_start: 0.8647 (p) cc_final: 0.8416 (p) REVERT: E 399 GLU cc_start: 0.8287 (pm20) cc_final: 0.7971 (pm20) REVERT: E 407 ARG cc_start: 0.8700 (ttt180) cc_final: 0.8059 (ttt90) REVERT: E 483 MET cc_start: 0.9459 (tmm) cc_final: 0.8466 (tmm) REVERT: E 487 GLU cc_start: 0.8902 (tt0) cc_final: 0.8609 (tt0) REVERT: E 512 ARG cc_start: 0.8692 (mtp-110) cc_final: 0.8336 (ttp-110) REVERT: F 16 ASP cc_start: 0.8764 (t0) cc_final: 0.8500 (t0) REVERT: F 28 ASP cc_start: 0.8699 (m-30) cc_final: 0.8443 (m-30) REVERT: F 75 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7781 (mm-30) REVERT: F 254 GLU cc_start: 0.8906 (tp30) cc_final: 0.8659 (tp30) REVERT: F 269 ASP cc_start: 0.8150 (m-30) cc_final: 0.7791 (m-30) REVERT: F 329 SER cc_start: 0.9482 (p) cc_final: 0.9216 (p) REVERT: F 393 THR cc_start: 0.8577 (p) cc_final: 0.8312 (p) REVERT: F 399 GLU cc_start: 0.8288 (pm20) cc_final: 0.7981 (pm20) REVERT: F 417 LEU cc_start: 0.8520 (pt) cc_final: 0.8194 (pt) REVERT: F 483 MET cc_start: 0.9444 (tmm) cc_final: 0.8469 (tmm) REVERT: F 487 GLU cc_start: 0.8880 (tt0) cc_final: 0.8595 (tt0) REVERT: G 16 ASP cc_start: 0.8720 (t0) cc_final: 0.8425 (t0) REVERT: G 28 ASP cc_start: 0.8485 (m-30) cc_final: 0.8227 (m-30) REVERT: G 75 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7804 (mm-30) REVERT: G 254 GLU cc_start: 0.8704 (tp30) cc_final: 0.8451 (tp30) REVERT: G 269 ASP cc_start: 0.8127 (m-30) cc_final: 0.7879 (m-30) REVERT: G 329 SER cc_start: 0.9450 (p) cc_final: 0.9155 (p) REVERT: G 399 GLU cc_start: 0.8308 (pm20) cc_final: 0.7971 (pm20) REVERT: G 483 MET cc_start: 0.9395 (tmm) cc_final: 0.8411 (tmm) REVERT: G 487 GLU cc_start: 0.8896 (tt0) cc_final: 0.8635 (tt0) REVERT: G 512 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8232 (ttp-110) REVERT: H 16 ASP cc_start: 0.8735 (t0) cc_final: 0.8352 (t0) REVERT: H 75 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7920 (mm-30) REVERT: H 80 ILE cc_start: 0.9520 (mt) cc_final: 0.9253 (mm) REVERT: H 84 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6398 (mt) REVERT: H 254 GLU cc_start: 0.8926 (tp30) cc_final: 0.8682 (tp30) REVERT: H 329 SER cc_start: 0.9471 (p) cc_final: 0.9192 (p) REVERT: H 399 GLU cc_start: 0.8291 (pm20) cc_final: 0.7957 (pm20) REVERT: H 483 MET cc_start: 0.9447 (tmm) cc_final: 0.8531 (tmm) REVERT: H 487 GLU cc_start: 0.8872 (tt0) cc_final: 0.8620 (tt0) REVERT: H 512 ARG cc_start: 0.8863 (ttp80) cc_final: 0.8517 (ttp80) outliers start: 89 outliers final: 42 residues processed: 594 average time/residue: 0.3065 time to fit residues: 292.6118 Evaluate side-chains 560 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 513 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** C 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** G 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 23376 Z= 0.463 Angle : 0.626 6.592 31640 Z= 0.316 Chirality : 0.047 0.144 3648 Planarity : 0.003 0.033 3976 Dihedral : 8.697 61.642 3724 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.84 % Allowed : 13.17 % Favored : 81.99 % 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: -1.00 (0.15), residues: 2952 helix: 0.29 (0.16), residues: 1088 sheet: -2.40 (0.20), residues: 472 loop : -0.66 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 372 PHE 0.009 0.001 PHE H 90 TYR 0.013 0.002 TYR H 353 ARG 0.003 0.001 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 524 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.8893 (tp30) cc_final: 0.8624 (tp30) REVERT: A 269 ASP cc_start: 0.8003 (m-30) cc_final: 0.7744 (m-30) REVERT: A 319 ASP cc_start: 0.8186 (m-30) cc_final: 0.7811 (m-30) REVERT: A 329 SER cc_start: 0.9539 (p) cc_final: 0.9253 (p) REVERT: A 352 GLU cc_start: 0.8655 (tp30) cc_final: 0.8435 (tp30) REVERT: A 399 GLU cc_start: 0.8434 (pm20) cc_final: 0.8140 (pm20) REVERT: A 483 MET cc_start: 0.9384 (tmm) cc_final: 0.8456 (tmm) REVERT: A 487 GLU cc_start: 0.8782 (tt0) cc_final: 0.8532 (tt0) REVERT: A 512 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.8204 (mtp-110) REVERT: B 28 ASP cc_start: 0.8725 (m-30) cc_final: 0.8355 (m-30) REVERT: B 254 GLU cc_start: 0.8966 (tp30) cc_final: 0.8689 (tp30) REVERT: B 319 ASP cc_start: 0.8120 (m-30) cc_final: 0.7712 (m-30) REVERT: B 335 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 385 MET cc_start: 0.8806 (ttm) cc_final: 0.8457 (ttp) REVERT: B 399 GLU cc_start: 0.8444 (pm20) cc_final: 0.8135 (pm20) REVERT: B 483 MET cc_start: 0.9439 (tmm) cc_final: 0.8579 (tmm) REVERT: B 487 GLU cc_start: 0.8748 (tt0) cc_final: 0.8474 (tt0) REVERT: C 28 ASP cc_start: 0.8799 (m-30) cc_final: 0.8588 (m-30) REVERT: C 75 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7981 (mm-30) REVERT: C 254 GLU cc_start: 0.8926 (tp30) cc_final: 0.8599 (tp30) REVERT: C 269 ASP cc_start: 0.8028 (m-30) cc_final: 0.7783 (m-30) REVERT: C 319 ASP cc_start: 0.8176 (m-30) cc_final: 0.7832 (m-30) REVERT: C 399 GLU cc_start: 0.8430 (pm20) cc_final: 0.8156 (pm20) REVERT: C 483 MET cc_start: 0.9416 (tmm) cc_final: 0.8435 (tmm) REVERT: C 487 GLU cc_start: 0.8799 (tt0) cc_final: 0.8573 (tt0) REVERT: C 512 ARG cc_start: 0.8628 (mtp-110) cc_final: 0.8150 (ttp-110) REVERT: D 25 ASN cc_start: 0.8987 (m-40) cc_final: 0.8107 (t0) REVERT: D 28 ASP cc_start: 0.8632 (m-30) cc_final: 0.8300 (m-30) REVERT: D 70 MET cc_start: 0.9047 (mtp) cc_final: 0.8625 (mtp) REVERT: D 319 ASP cc_start: 0.8166 (m-30) cc_final: 0.7738 (m-30) REVERT: D 335 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7050 (tm-30) REVERT: D 399 GLU cc_start: 0.8431 (pm20) cc_final: 0.8136 (pm20) REVERT: D 487 GLU cc_start: 0.8783 (tt0) cc_final: 0.8445 (tt0) REVERT: E 28 ASP cc_start: 0.8760 (m-30) cc_final: 0.8526 (m-30) REVERT: E 33 ASN cc_start: 0.8504 (p0) cc_final: 0.8294 (p0) REVERT: E 75 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7758 (mm-30) REVERT: E 84 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6977 (mm) REVERT: E 98 GLU cc_start: 0.8802 (pm20) cc_final: 0.8449 (mp0) REVERT: E 269 ASP cc_start: 0.8014 (m-30) cc_final: 0.7746 (m-30) REVERT: E 329 SER cc_start: 0.9413 (p) cc_final: 0.9072 (p) REVERT: E 399 GLU cc_start: 0.8421 (pm20) cc_final: 0.8123 (pm20) REVERT: E 412 ARG cc_start: 0.8467 (ptp-170) cc_final: 0.8084 (ptp-170) REVERT: E 483 MET cc_start: 0.9421 (tmm) cc_final: 0.8557 (tmm) REVERT: E 487 GLU cc_start: 0.8879 (tt0) cc_final: 0.8634 (tt0) REVERT: E 512 ARG cc_start: 0.8637 (mtp-110) cc_final: 0.8208 (ttp-110) REVERT: F 16 ASP cc_start: 0.8752 (t0) cc_final: 0.8457 (t0) REVERT: F 28 ASP cc_start: 0.8781 (m-30) cc_final: 0.8547 (m-30) REVERT: F 33 ASN cc_start: 0.8462 (p0) cc_final: 0.8257 (p0) REVERT: F 75 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7973 (mm-30) REVERT: F 80 ILE cc_start: 0.9316 (pt) cc_final: 0.9064 (mm) REVERT: F 319 ASP cc_start: 0.8125 (m-30) cc_final: 0.7686 (m-30) REVERT: F 329 SER cc_start: 0.9422 (p) cc_final: 0.9113 (p) REVERT: F 399 GLU cc_start: 0.8428 (pm20) cc_final: 0.8090 (pm20) REVERT: F 417 LEU cc_start: 0.8647 (pt) cc_final: 0.8396 (pt) REVERT: F 483 MET cc_start: 0.9433 (tmm) cc_final: 0.8534 (tmm) REVERT: F 487 GLU cc_start: 0.8780 (tt0) cc_final: 0.8556 (tt0) REVERT: G 28 ASP cc_start: 0.8597 (m-30) cc_final: 0.8254 (m-30) REVERT: G 75 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8070 (mm-30) REVERT: G 105 ARG cc_start: 0.8731 (tmm160) cc_final: 0.8304 (ttp80) REVERT: G 269 ASP cc_start: 0.8094 (m-30) cc_final: 0.7831 (m-30) REVERT: G 319 ASP cc_start: 0.8110 (m-30) cc_final: 0.7758 (m-30) REVERT: G 329 SER cc_start: 0.9374 (p) cc_final: 0.9040 (p) REVERT: G 399 GLU cc_start: 0.8427 (pm20) cc_final: 0.8114 (pm20) REVERT: G 483 MET cc_start: 0.9380 (tmm) cc_final: 0.8477 (tmm) REVERT: G 487 GLU cc_start: 0.8808 (tt0) cc_final: 0.8564 (tt0) REVERT: G 512 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.8237 (ttp80) REVERT: H 28 ASP cc_start: 0.8636 (m-30) cc_final: 0.8392 (m-30) REVERT: H 70 MET cc_start: 0.9051 (mtp) cc_final: 0.8617 (mtp) REVERT: H 75 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8107 (mm-30) REVERT: H 254 GLU cc_start: 0.8958 (tp30) cc_final: 0.8707 (tp30) REVERT: H 319 ASP cc_start: 0.8120 (m-30) cc_final: 0.7691 (m-30) REVERT: H 329 SER cc_start: 0.9474 (p) cc_final: 0.9175 (p) REVERT: H 335 GLU cc_start: 0.7752 (tm-30) cc_final: 0.6998 (tm-30) REVERT: H 352 GLU cc_start: 0.8575 (tp30) cc_final: 0.8369 (tp30) REVERT: H 399 GLU cc_start: 0.8418 (pm20) cc_final: 0.8108 (pm20) REVERT: H 483 MET cc_start: 0.9425 (tmm) cc_final: 0.8564 (tmm) REVERT: H 487 GLU cc_start: 0.8837 (tt0) cc_final: 0.8591 (tt0) REVERT: H 512 ARG cc_start: 0.8883 (ttp80) cc_final: 0.8338 (ttp80) outliers start: 115 outliers final: 76 residues processed: 598 average time/residue: 0.3266 time to fit residues: 312.7610 Evaluate side-chains 577 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 500 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 500 GLU 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: 0.9990 chunk 167 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 286 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** C 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** G 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23376 Z= 0.221 Angle : 0.518 7.544 31640 Z= 0.262 Chirality : 0.042 0.137 3648 Planarity : 0.003 0.033 3976 Dihedral : 8.166 59.600 3724 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.41 % Allowed : 15.66 % Favored : 80.93 % 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: -0.79 (0.15), residues: 2952 helix: 0.51 (0.16), residues: 1088 sheet: -2.16 (0.19), residues: 488 loop : -0.61 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 372 PHE 0.011 0.001 PHE G 401 TYR 0.009 0.001 TYR H 353 ARG 0.003 0.000 ARG D 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 540 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8695 (t0) cc_final: 0.8394 (t0) REVERT: A 75 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 254 GLU cc_start: 0.8888 (tp30) cc_final: 0.8585 (tp30) REVERT: A 269 ASP cc_start: 0.8046 (m-30) cc_final: 0.7787 (m-30) REVERT: A 399 GLU cc_start: 0.8425 (pm20) cc_final: 0.8160 (pm20) REVERT: A 420 MET cc_start: 0.5885 (ttm) cc_final: 0.5647 (mtp) REVERT: A 483 MET cc_start: 0.9384 (tmm) cc_final: 0.8415 (tmm) REVERT: A 487 GLU cc_start: 0.8843 (tt0) cc_final: 0.8624 (tt0) REVERT: A 512 ARG cc_start: 0.8597 (mtp-110) cc_final: 0.8212 (mtp-110) REVERT: B 28 ASP cc_start: 0.8671 (m-30) cc_final: 0.8414 (m-30) REVERT: B 75 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 84 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6880 (mm) REVERT: B 254 GLU cc_start: 0.8881 (tp30) cc_final: 0.8580 (tp30) REVERT: B 385 MET cc_start: 0.8756 (ttm) cc_final: 0.8383 (ttp) REVERT: B 399 GLU cc_start: 0.8404 (pm20) cc_final: 0.8113 (pm20) REVERT: B 483 MET cc_start: 0.9461 (tmm) cc_final: 0.8523 (tmm) REVERT: B 487 GLU cc_start: 0.8813 (tt0) cc_final: 0.8600 (tt0) REVERT: C 16 ASP cc_start: 0.8695 (t0) cc_final: 0.8382 (t0) REVERT: C 28 ASP cc_start: 0.8737 (m-30) cc_final: 0.8526 (m-30) REVERT: C 75 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7902 (mm-30) REVERT: C 84 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7071 (mt) REVERT: C 254 GLU cc_start: 0.8878 (tp30) cc_final: 0.8535 (tp30) REVERT: C 399 GLU cc_start: 0.8408 (pm20) cc_final: 0.8171 (pm20) REVERT: C 483 MET cc_start: 0.9406 (tmm) cc_final: 0.8458 (tmm) REVERT: C 512 ARG cc_start: 0.8608 (mtp-110) cc_final: 0.8290 (ttp80) REVERT: D 16 ASP cc_start: 0.8775 (t0) cc_final: 0.8491 (t0) REVERT: D 25 ASN cc_start: 0.8928 (m-40) cc_final: 0.8071 (t0) REVERT: D 28 ASP cc_start: 0.8543 (m-30) cc_final: 0.8230 (m-30) REVERT: D 70 MET cc_start: 0.8994 (mtp) cc_final: 0.8657 (mtp) REVERT: D 399 GLU cc_start: 0.8412 (pm20) cc_final: 0.8158 (pm20) REVERT: D 410 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8328 (ttmm) REVERT: D 512 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8550 (ttp-110) REVERT: E 16 ASP cc_start: 0.8687 (t0) cc_final: 0.8389 (t0) REVERT: E 28 ASP cc_start: 0.8708 (m-30) cc_final: 0.8488 (m-30) REVERT: E 75 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7825 (mm-30) REVERT: E 84 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7184 (mt) REVERT: E 98 GLU cc_start: 0.8759 (pm20) cc_final: 0.8416 (mp0) REVERT: E 256 ASP cc_start: 0.8989 (m-30) cc_final: 0.8743 (t0) REVERT: E 269 ASP cc_start: 0.8031 (m-30) cc_final: 0.7798 (m-30) REVERT: E 329 SER cc_start: 0.9512 (p) cc_final: 0.9204 (p) REVERT: E 399 GLU cc_start: 0.8393 (pm20) cc_final: 0.8142 (pm20) REVERT: E 407 ARG cc_start: 0.8706 (ttp80) cc_final: 0.7450 (ttt90) REVERT: E 412 ARG cc_start: 0.8532 (ptp-170) cc_final: 0.8193 (ptp-170) REVERT: E 483 MET cc_start: 0.9445 (tmm) cc_final: 0.8490 (tmm) REVERT: E 512 ARG cc_start: 0.8657 (mtp-110) cc_final: 0.8261 (ttp-110) REVERT: F 28 ASP cc_start: 0.8754 (m-30) cc_final: 0.8527 (m-30) REVERT: F 75 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7998 (mm-30) REVERT: F 80 ILE cc_start: 0.9309 (pt) cc_final: 0.9058 (mm) REVERT: F 84 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6357 (mt) REVERT: F 329 SER cc_start: 0.9490 (p) cc_final: 0.9202 (p) REVERT: F 399 GLU cc_start: 0.8388 (pm20) cc_final: 0.8086 (pm20) REVERT: F 417 LEU cc_start: 0.8596 (pt) cc_final: 0.8214 (pt) REVERT: G 16 ASP cc_start: 0.8687 (t0) cc_final: 0.8371 (t0) REVERT: G 28 ASP cc_start: 0.8475 (m-30) cc_final: 0.8149 (m-30) REVERT: G 75 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7784 (mm-30) REVERT: G 105 ARG cc_start: 0.8684 (tmm160) cc_final: 0.8294 (ttp80) REVERT: G 269 ASP cc_start: 0.8083 (m-30) cc_final: 0.7858 (m-30) REVERT: G 329 SER cc_start: 0.9472 (p) cc_final: 0.9157 (p) REVERT: G 399 GLU cc_start: 0.8405 (pm20) cc_final: 0.8130 (pm20) REVERT: G 410 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8328 (ttmm) REVERT: G 483 MET cc_start: 0.9381 (tmm) cc_final: 0.8463 (tmm) REVERT: G 487 GLU cc_start: 0.8854 (tt0) cc_final: 0.8633 (tt0) REVERT: G 512 ARG cc_start: 0.8608 (mtp-110) cc_final: 0.8281 (ttp80) REVERT: H 16 ASP cc_start: 0.8742 (t0) cc_final: 0.8477 (t0) REVERT: H 28 ASP cc_start: 0.8570 (m-30) cc_final: 0.8315 (m-30) REVERT: H 70 MET cc_start: 0.8999 (mtp) cc_final: 0.8568 (mtp) REVERT: H 75 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8112 (mm-30) REVERT: H 254 GLU cc_start: 0.8946 (tp30) cc_final: 0.8697 (tp30) REVERT: H 329 SER cc_start: 0.9536 (p) cc_final: 0.9263 (p) REVERT: H 352 GLU cc_start: 0.8446 (tp30) cc_final: 0.8196 (tp30) REVERT: H 399 GLU cc_start: 0.8390 (pm20) cc_final: 0.8100 (pm20) REVERT: H 483 MET cc_start: 0.9447 (tmm) cc_final: 0.8496 (tmm) outliers start: 81 outliers final: 56 residues processed: 594 average time/residue: 0.3228 time to fit residues: 308.4436 Evaluate side-chains 573 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 513 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 285 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 131 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23376 Z= 0.199 Angle : 0.506 7.779 31640 Z= 0.255 Chirality : 0.041 0.135 3648 Planarity : 0.003 0.034 3976 Dihedral : 7.969 61.749 3724 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.70 % Allowed : 15.78 % Favored : 80.51 % 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: -0.66 (0.15), residues: 2952 helix: 0.59 (0.16), residues: 1088 sheet: -2.01 (0.20), residues: 488 loop : -0.53 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 92 PHE 0.010 0.001 PHE H 401 TYR 0.009 0.001 TYR D 348 ARG 0.003 0.000 ARG H 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 525 time to evaluate : 2.770 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8661 (t0) cc_final: 0.8369 (t0) REVERT: A 84 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6522 (mm) REVERT: A 254 GLU cc_start: 0.8882 (tp30) cc_final: 0.8579 (tp30) REVERT: A 269 ASP cc_start: 0.8005 (m-30) cc_final: 0.7765 (m-30) REVERT: A 399 GLU cc_start: 0.8398 (pm20) cc_final: 0.8143 (pm20) REVERT: A 483 MET cc_start: 0.9373 (tmm) cc_final: 0.8436 (tmm) REVERT: A 512 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8214 (mtp-110) REVERT: B 28 ASP cc_start: 0.8631 (m-30) cc_final: 0.8377 (m-30) REVERT: B 36 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7549 (pp) REVERT: B 75 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 84 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6482 (mm) REVERT: B 102 ASN cc_start: 0.9205 (t0) cc_final: 0.8755 (t0) REVERT: B 105 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8229 (ttp80) REVERT: B 254 GLU cc_start: 0.8835 (tp30) cc_final: 0.8527 (tp30) REVERT: B 385 MET cc_start: 0.8704 (ttm) cc_final: 0.8334 (ttp) REVERT: B 399 GLU cc_start: 0.8454 (pm20) cc_final: 0.8186 (pm20) REVERT: B 410 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8370 (ttmm) REVERT: B 483 MET cc_start: 0.9458 (tmm) cc_final: 0.8543 (tmm) REVERT: C 16 ASP cc_start: 0.8706 (t0) cc_final: 0.8398 (t0) REVERT: C 75 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7907 (mm-30) REVERT: C 84 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7279 (mt) REVERT: C 254 GLU cc_start: 0.8873 (tp30) cc_final: 0.8517 (tp30) REVERT: C 399 GLU cc_start: 0.8407 (pm20) cc_final: 0.8162 (pm20) REVERT: C 483 MET cc_start: 0.9396 (tmm) cc_final: 0.8482 (tmm) REVERT: C 512 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.8271 (ttp80) REVERT: D 16 ASP cc_start: 0.8781 (t0) cc_final: 0.8469 (t0) REVERT: D 28 ASP cc_start: 0.8531 (m-30) cc_final: 0.8239 (m-30) REVERT: D 36 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7437 (pp) REVERT: D 70 MET cc_start: 0.8998 (mtp) cc_final: 0.8646 (mtp) REVERT: D 399 GLU cc_start: 0.8422 (pm20) cc_final: 0.8171 (pm20) REVERT: D 410 LYS cc_start: 0.8621 (ptpp) cc_final: 0.8385 (ttmm) REVERT: D 512 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8406 (ttp80) REVERT: E 16 ASP cc_start: 0.8679 (t0) cc_final: 0.8376 (t0) REVERT: E 75 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7864 (mm-30) REVERT: E 84 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7229 (mt) REVERT: E 98 GLU cc_start: 0.8736 (pm20) cc_final: 0.8400 (mp0) REVERT: E 103 GLU cc_start: 0.8766 (tp30) cc_final: 0.7726 (mm-30) REVERT: E 256 ASP cc_start: 0.8902 (m-30) cc_final: 0.8651 (t0) REVERT: E 269 ASP cc_start: 0.7985 (m-30) cc_final: 0.7750 (m-30) REVERT: E 329 SER cc_start: 0.9514 (p) cc_final: 0.9211 (p) REVERT: E 399 GLU cc_start: 0.8404 (pm20) cc_final: 0.8144 (pm20) REVERT: E 407 ARG cc_start: 0.8749 (ttp80) cc_final: 0.7557 (ttt90) REVERT: E 412 ARG cc_start: 0.8630 (ptp-170) cc_final: 0.8327 (ptp-170) REVERT: E 483 MET cc_start: 0.9393 (tmm) cc_final: 0.8606 (tmm) REVERT: E 512 ARG cc_start: 0.8637 (mtp-110) cc_final: 0.8276 (ttp-110) REVERT: F 16 ASP cc_start: 0.8703 (t0) cc_final: 0.8487 (t0) REVERT: F 28 ASP cc_start: 0.8728 (m-30) cc_final: 0.8505 (m-30) REVERT: F 75 GLU cc_start: 0.8237 (mm-30) cc_final: 0.8028 (mm-30) REVERT: F 84 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6425 (mt) REVERT: F 98 GLU cc_start: 0.8759 (pm20) cc_final: 0.8519 (pm20) REVERT: F 329 SER cc_start: 0.9489 (p) cc_final: 0.9220 (p) REVERT: F 399 GLU cc_start: 0.8432 (pm20) cc_final: 0.8146 (pm20) REVERT: F 410 LYS cc_start: 0.8559 (ptpp) cc_final: 0.8345 (ttmm) REVERT: F 417 LEU cc_start: 0.8565 (pt) cc_final: 0.8155 (pt) REVERT: F 483 MET cc_start: 0.9402 (tmm) cc_final: 0.8484 (tmm) REVERT: G 16 ASP cc_start: 0.8642 (t0) cc_final: 0.8335 (t0) REVERT: G 75 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7862 (mm-30) REVERT: G 84 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6437 (mm) REVERT: G 103 GLU cc_start: 0.8863 (tp30) cc_final: 0.8605 (mm-30) REVERT: G 105 ARG cc_start: 0.8711 (tmm160) cc_final: 0.8300 (ttp80) REVERT: G 269 ASP cc_start: 0.7995 (m-30) cc_final: 0.7788 (m-30) REVERT: G 329 SER cc_start: 0.9470 (p) cc_final: 0.9158 (p) REVERT: G 399 GLU cc_start: 0.8415 (pm20) cc_final: 0.8143 (pm20) REVERT: G 410 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8332 (ttmm) REVERT: G 483 MET cc_start: 0.9377 (tmm) cc_final: 0.8503 (tmm) REVERT: G 512 ARG cc_start: 0.8610 (mtp-110) cc_final: 0.8291 (ttp80) REVERT: H 16 ASP cc_start: 0.8717 (t0) cc_final: 0.8466 (t0) REVERT: H 28 ASP cc_start: 0.8535 (m-30) cc_final: 0.8293 (m-30) REVERT: H 70 MET cc_start: 0.8980 (mtp) cc_final: 0.8570 (mtp) REVERT: H 75 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7956 (mm-30) REVERT: H 254 GLU cc_start: 0.8924 (tp30) cc_final: 0.8670 (tp30) REVERT: H 329 SER cc_start: 0.9540 (p) cc_final: 0.9264 (p) REVERT: H 399 GLU cc_start: 0.8442 (pm20) cc_final: 0.8152 (pm20) REVERT: H 483 MET cc_start: 0.9437 (tmm) cc_final: 0.8521 (tmm) outliers start: 88 outliers final: 54 residues processed: 584 average time/residue: 0.3354 time to fit residues: 315.9071 Evaluate side-chains 567 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 505 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 3.9990 chunk 113 optimal weight: 0.0370 chunk 170 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN E 102 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23376 Z= 0.149 Angle : 0.484 7.634 31640 Z= 0.244 Chirality : 0.040 0.134 3648 Planarity : 0.003 0.034 3976 Dihedral : 7.746 59.808 3724 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.95 % Allowed : 16.84 % Favored : 80.22 % 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: -0.51 (0.15), residues: 2952 helix: 0.69 (0.16), residues: 1088 sheet: -2.02 (0.21), residues: 472 loop : -0.42 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 92 PHE 0.010 0.001 PHE A 401 TYR 0.011 0.001 TYR B 12 ARG 0.003 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 541 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8695 (t0) cc_final: 0.8361 (t0) REVERT: A 25 ASN cc_start: 0.8861 (m-40) cc_final: 0.7886 (t0) REVERT: A 36 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7474 (pp) REVERT: A 75 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 84 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6833 (mm) REVERT: A 254 GLU cc_start: 0.8878 (tp30) cc_final: 0.8565 (tp30) REVERT: A 269 ASP cc_start: 0.8031 (m-30) cc_final: 0.7764 (m-30) REVERT: A 335 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7397 (tt0) REVERT: A 410 LYS cc_start: 0.8666 (ptpp) cc_final: 0.8376 (ttmm) REVERT: A 487 GLU cc_start: 0.8828 (tt0) cc_final: 0.8623 (tt0) REVERT: A 512 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8219 (mtp-110) REVERT: B 28 ASP cc_start: 0.8620 (m-30) cc_final: 0.8390 (m-30) REVERT: B 36 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7522 (pp) REVERT: B 75 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8026 (mm-30) REVERT: B 78 MET cc_start: 0.9260 (tpp) cc_final: 0.8973 (tpp) REVERT: B 84 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6826 (mm) REVERT: B 254 GLU cc_start: 0.8804 (tp30) cc_final: 0.8413 (tp30) REVERT: B 385 MET cc_start: 0.8660 (ttm) cc_final: 0.8287 (ttp) REVERT: B 399 GLU cc_start: 0.8431 (pm20) cc_final: 0.8188 (pm20) REVERT: B 410 LYS cc_start: 0.8696 (ptpp) cc_final: 0.8464 (ttmm) REVERT: B 483 MET cc_start: 0.9457 (tmm) cc_final: 0.8481 (tmm) REVERT: C 16 ASP cc_start: 0.8715 (t0) cc_final: 0.8427 (t0) REVERT: C 25 ASN cc_start: 0.8767 (m-40) cc_final: 0.7799 (t0) REVERT: C 36 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7536 (pp) REVERT: C 75 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7905 (mm-30) REVERT: C 78 MET cc_start: 0.9362 (tpp) cc_final: 0.9127 (tpp) REVERT: C 84 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6883 (mt) REVERT: C 254 GLU cc_start: 0.8868 (tp30) cc_final: 0.8501 (tp30) REVERT: C 335 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7409 (tt0) REVERT: C 393 THR cc_start: 0.8769 (p) cc_final: 0.8529 (p) REVERT: C 399 GLU cc_start: 0.8338 (pm20) cc_final: 0.8123 (pm20) REVERT: C 483 MET cc_start: 0.9401 (tmm) cc_final: 0.8435 (tmm) REVERT: C 512 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.8258 (ttp80) REVERT: D 16 ASP cc_start: 0.8768 (t0) cc_final: 0.8394 (t0) REVERT: D 36 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7475 (pp) REVERT: D 70 MET cc_start: 0.8927 (mtp) cc_final: 0.8622 (mtp) REVERT: D 78 MET cc_start: 0.9322 (tpp) cc_final: 0.9066 (tpp) REVERT: D 399 GLU cc_start: 0.8393 (pm20) cc_final: 0.8168 (pm20) REVERT: D 410 LYS cc_start: 0.8686 (ptpp) cc_final: 0.8450 (ttmm) REVERT: E 16 ASP cc_start: 0.8664 (t0) cc_final: 0.8422 (t0) REVERT: E 36 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7614 (pp) REVERT: E 75 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7916 (mm-30) REVERT: E 84 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6815 (mt) REVERT: E 98 GLU cc_start: 0.8688 (pm20) cc_final: 0.8351 (mp0) REVERT: E 102 ASN cc_start: 0.9064 (t0) cc_final: 0.8727 (t0) REVERT: E 105 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8169 (ttp80) REVERT: E 256 ASP cc_start: 0.8794 (m-30) cc_final: 0.8494 (t0) REVERT: E 269 ASP cc_start: 0.7957 (m-30) cc_final: 0.7725 (m-30) REVERT: E 335 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7331 (tt0) REVERT: E 364 ASP cc_start: 0.8306 (p0) cc_final: 0.8086 (p0) REVERT: E 368 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8453 (mp10) REVERT: E 399 GLU cc_start: 0.8385 (pm20) cc_final: 0.8117 (pm20) REVERT: E 412 ARG cc_start: 0.8586 (ptp-170) cc_final: 0.8355 (ptp-170) REVERT: E 483 MET cc_start: 0.9382 (tmm) cc_final: 0.8564 (tmm) REVERT: E 487 GLU cc_start: 0.8812 (tt0) cc_final: 0.8610 (tt0) REVERT: E 512 ARG cc_start: 0.8638 (mtp-110) cc_final: 0.8239 (ttp-110) REVERT: F 16 ASP cc_start: 0.8691 (t0) cc_final: 0.8463 (t0) REVERT: F 25 ASN cc_start: 0.8911 (m-40) cc_final: 0.7964 (t0) REVERT: F 28 ASP cc_start: 0.8710 (m-30) cc_final: 0.8484 (m-30) REVERT: F 84 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6696 (mt) REVERT: F 329 SER cc_start: 0.9513 (p) cc_final: 0.9251 (p) REVERT: F 335 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7468 (tt0) REVERT: F 393 THR cc_start: 0.8519 (p) cc_final: 0.8290 (p) REVERT: F 399 GLU cc_start: 0.8383 (pm20) cc_final: 0.8135 (pm20) REVERT: F 410 LYS cc_start: 0.8662 (ptpp) cc_final: 0.8439 (ttmm) REVERT: F 417 LEU cc_start: 0.8454 (pt) cc_final: 0.8109 (pt) REVERT: F 483 MET cc_start: 0.9406 (tmm) cc_final: 0.8405 (tmm) REVERT: G 16 ASP cc_start: 0.8648 (t0) cc_final: 0.8403 (t0) REVERT: G 25 ASN cc_start: 0.8698 (m-40) cc_final: 0.7723 (t0) REVERT: G 75 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7933 (mm-30) REVERT: G 84 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6524 (mm) REVERT: G 103 GLU cc_start: 0.8833 (tp30) cc_final: 0.7937 (mm-30) REVERT: G 105 ARG cc_start: 0.8620 (tmm160) cc_final: 0.8372 (ttp80) REVERT: G 335 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7398 (tt0) REVERT: G 399 GLU cc_start: 0.8372 (pm20) cc_final: 0.8134 (pm20) REVERT: G 410 LYS cc_start: 0.8656 (ptpp) cc_final: 0.8403 (ttmm) REVERT: G 420 MET cc_start: 0.5913 (ttm) cc_final: 0.5697 (mtp) REVERT: G 483 MET cc_start: 0.9378 (tmm) cc_final: 0.8513 (tmm) REVERT: G 512 ARG cc_start: 0.8615 (mtp-110) cc_final: 0.8316 (ttp80) REVERT: H 16 ASP cc_start: 0.8735 (t0) cc_final: 0.8362 (t0) REVERT: H 28 ASP cc_start: 0.8464 (m-30) cc_final: 0.8235 (m-30) REVERT: H 36 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7405 (pp) REVERT: H 70 MET cc_start: 0.8928 (mtp) cc_final: 0.8568 (mtp) REVERT: H 75 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7924 (mm-30) REVERT: H 78 MET cc_start: 0.9299 (tpp) cc_final: 0.9006 (tpp) REVERT: H 254 GLU cc_start: 0.8923 (tp30) cc_final: 0.8682 (tp30) REVERT: H 399 GLU cc_start: 0.8394 (pm20) cc_final: 0.8139 (pm20) REVERT: H 483 MET cc_start: 0.9425 (tmm) cc_final: 0.8540 (tmm) REVERT: H 512 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8241 (ttp80) outliers start: 70 outliers final: 42 residues processed: 582 average time/residue: 0.3025 time to fit residues: 281.8224 Evaluate side-chains 570 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 515 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 500 GLU 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: 0.9980 chunk 160 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 240 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 264 optimal weight: 0.6980 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23376 Z= 0.219 Angle : 0.512 7.423 31640 Z= 0.258 Chirality : 0.042 0.141 3648 Planarity : 0.003 0.033 3976 Dihedral : 7.743 58.490 3724 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.78 % Allowed : 18.14 % Favored : 79.08 % 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: -0.48 (0.15), residues: 2952 helix: 0.71 (0.16), residues: 1088 sheet: -1.76 (0.21), residues: 488 loop : -0.47 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 454 PHE 0.010 0.001 PHE C 401 TYR 0.011 0.001 TYR F 12 ARG 0.003 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 507 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8684 (t0) cc_final: 0.8353 (t0) REVERT: A 25 ASN cc_start: 0.8814 (m-40) cc_final: 0.7818 (t0) REVERT: A 36 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7555 (pp) REVERT: A 84 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6793 (mm) REVERT: A 254 GLU cc_start: 0.8886 (tp30) cc_final: 0.8577 (tp30) REVERT: A 269 ASP cc_start: 0.8036 (m-30) cc_final: 0.7748 (m-30) REVERT: A 335 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7401 (tt0) REVERT: A 410 LYS cc_start: 0.8663 (ptpp) cc_final: 0.8398 (ttmm) REVERT: A 487 GLU cc_start: 0.8827 (tt0) cc_final: 0.8620 (tt0) REVERT: A 512 ARG cc_start: 0.8602 (mtp-110) cc_final: 0.8209 (mtp-110) REVERT: B 25 ASN cc_start: 0.8903 (m-40) cc_final: 0.7801 (t0) REVERT: B 28 ASP cc_start: 0.8630 (m-30) cc_final: 0.8419 (m-30) REVERT: B 36 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7667 (pp) REVERT: B 75 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7979 (mm-30) REVERT: B 84 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6857 (mm) REVERT: B 254 GLU cc_start: 0.8799 (tp30) cc_final: 0.8404 (tp30) REVERT: B 385 MET cc_start: 0.8735 (ttm) cc_final: 0.8369 (ttp) REVERT: B 399 GLU cc_start: 0.8449 (pm20) cc_final: 0.8202 (pm20) REVERT: B 410 LYS cc_start: 0.8720 (ptpp) cc_final: 0.8481 (ttmm) REVERT: B 483 MET cc_start: 0.9440 (tmm) cc_final: 0.8523 (tmm) REVERT: C 16 ASP cc_start: 0.8711 (t0) cc_final: 0.8468 (t0) REVERT: C 25 ASN cc_start: 0.8785 (m-40) cc_final: 0.7810 (t0) REVERT: C 36 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7545 (pp) REVERT: C 75 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7827 (mm-30) REVERT: C 84 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7411 (mm) REVERT: C 254 GLU cc_start: 0.8872 (tp30) cc_final: 0.8531 (tp30) REVERT: C 335 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7408 (tt0) REVERT: C 399 GLU cc_start: 0.8359 (pm20) cc_final: 0.8149 (pm20) REVERT: C 410 LYS cc_start: 0.8632 (ptpp) cc_final: 0.8355 (ttmm) REVERT: C 483 MET cc_start: 0.9366 (tmm) cc_final: 0.8446 (tmm) REVERT: C 512 ARG cc_start: 0.8620 (mtp-110) cc_final: 0.8252 (ttp80) REVERT: D 16 ASP cc_start: 0.8791 (t0) cc_final: 0.8456 (t0) REVERT: D 36 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7525 (pp) REVERT: D 70 MET cc_start: 0.9023 (mtp) cc_final: 0.8756 (mtp) REVERT: D 78 MET cc_start: 0.9255 (tpp) cc_final: 0.9026 (tpp) REVERT: D 103 GLU cc_start: 0.8879 (tp30) cc_final: 0.8338 (mm-30) REVERT: D 399 GLU cc_start: 0.8411 (pm20) cc_final: 0.8184 (pm20) REVERT: D 410 LYS cc_start: 0.8738 (ptpp) cc_final: 0.8484 (ttmm) REVERT: D 512 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8658 (ttp80) REVERT: E 16 ASP cc_start: 0.8669 (t0) cc_final: 0.8418 (t0) REVERT: E 25 ASN cc_start: 0.8853 (m-40) cc_final: 0.7836 (t0) REVERT: E 36 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7576 (pp) REVERT: E 75 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7851 (mm-30) REVERT: E 84 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7351 (mm) REVERT: E 98 GLU cc_start: 0.8706 (pm20) cc_final: 0.8375 (mp0) REVERT: E 256 ASP cc_start: 0.8794 (m-30) cc_final: 0.8490 (t0) REVERT: E 269 ASP cc_start: 0.8049 (m-30) cc_final: 0.7808 (m-30) REVERT: E 335 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7348 (tt0) REVERT: E 368 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: E 399 GLU cc_start: 0.8409 (pm20) cc_final: 0.8169 (pm20) REVERT: E 412 ARG cc_start: 0.8617 (ptp-170) cc_final: 0.8353 (ptp-170) REVERT: E 483 MET cc_start: 0.9417 (tmm) cc_final: 0.8564 (tmm) REVERT: E 487 GLU cc_start: 0.8834 (tt0) cc_final: 0.8616 (tt0) REVERT: E 512 ARG cc_start: 0.8650 (mtp-110) cc_final: 0.8269 (ttp-110) REVERT: F 16 ASP cc_start: 0.8705 (t0) cc_final: 0.8459 (t0) REVERT: F 25 ASN cc_start: 0.8891 (m-40) cc_final: 0.7934 (t0) REVERT: F 36 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7713 (pp) REVERT: F 84 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6744 (mt) REVERT: F 329 SER cc_start: 0.9513 (p) cc_final: 0.9242 (p) REVERT: F 335 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7454 (tt0) REVERT: F 393 THR cc_start: 0.8668 (p) cc_final: 0.8454 (p) REVERT: F 399 GLU cc_start: 0.8404 (pm20) cc_final: 0.8145 (pm20) REVERT: F 410 LYS cc_start: 0.8683 (ptpp) cc_final: 0.8465 (ttmm) REVERT: F 417 LEU cc_start: 0.8478 (pt) cc_final: 0.8255 (pt) REVERT: F 483 MET cc_start: 0.9396 (tmm) cc_final: 0.8452 (tmm) REVERT: G 16 ASP cc_start: 0.8654 (t0) cc_final: 0.8406 (t0) REVERT: G 25 ASN cc_start: 0.8693 (m-40) cc_final: 0.7712 (t0) REVERT: G 36 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7536 (pp) REVERT: G 75 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7846 (mm-30) REVERT: G 84 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6574 (mm) REVERT: G 103 GLU cc_start: 0.8852 (tp30) cc_final: 0.8593 (mm-30) REVERT: G 105 ARG cc_start: 0.8628 (tmm160) cc_final: 0.8383 (ttp80) REVERT: G 335 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7405 (tt0) REVERT: G 399 GLU cc_start: 0.8400 (pm20) cc_final: 0.8138 (pm20) REVERT: G 410 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8453 (ttmm) REVERT: G 512 ARG cc_start: 0.8616 (mtp-110) cc_final: 0.8272 (ttp80) REVERT: H 16 ASP cc_start: 0.8712 (t0) cc_final: 0.8358 (t0) REVERT: H 25 ASN cc_start: 0.8898 (m-40) cc_final: 0.7844 (t0) REVERT: H 36 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7508 (pp) REVERT: H 70 MET cc_start: 0.8993 (mtp) cc_final: 0.8665 (mtp) REVERT: H 75 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7934 (mm-30) REVERT: H 102 ASN cc_start: 0.9114 (t0) cc_final: 0.8455 (t0) REVERT: H 105 ARG cc_start: 0.8709 (ttp-110) cc_final: 0.7935 (ttp-110) REVERT: H 254 GLU cc_start: 0.8921 (tp30) cc_final: 0.8691 (tp30) REVERT: H 399 GLU cc_start: 0.8416 (pm20) cc_final: 0.8158 (pm20) REVERT: H 483 MET cc_start: 0.9410 (tmm) cc_final: 0.8584 (tmm) outliers start: 66 outliers final: 45 residues processed: 547 average time/residue: 0.3264 time to fit residues: 286.1986 Evaluate side-chains 554 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 494 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.8980 chunk 281 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 133 optimal weight: 0.1980 chunk 195 optimal weight: 4.9990 chunk 294 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23376 Z= 0.215 Angle : 0.520 8.054 31640 Z= 0.262 Chirality : 0.042 0.140 3648 Planarity : 0.003 0.034 3976 Dihedral : 7.724 58.957 3724 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.61 % Allowed : 18.69 % Favored : 78.70 % 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: -0.45 (0.15), residues: 2952 helix: 0.70 (0.16), residues: 1088 sheet: -1.67 (0.21), residues: 488 loop : -0.46 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 454 PHE 0.010 0.001 PHE C 401 TYR 0.010 0.001 TYR F 348 ARG 0.004 0.000 ARG H 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 504 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8693 (t0) cc_final: 0.8431 (t0) REVERT: A 25 ASN cc_start: 0.8734 (m-40) cc_final: 0.7769 (t0) REVERT: A 36 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7500 (pp) REVERT: A 84 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6834 (mm) REVERT: A 98 GLU cc_start: 0.8747 (pm20) cc_final: 0.8545 (mp0) REVERT: A 254 GLU cc_start: 0.8901 (tp30) cc_final: 0.8670 (tp30) REVERT: A 269 ASP cc_start: 0.8072 (m-30) cc_final: 0.7728 (m-30) REVERT: A 335 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7404 (tt0) REVERT: A 410 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8410 (ttmm) REVERT: A 483 MET cc_start: 0.9476 (tmm) cc_final: 0.8443 (tmm) REVERT: A 487 GLU cc_start: 0.8841 (tt0) cc_final: 0.8579 (tt0) REVERT: A 512 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8215 (mtp-110) REVERT: B 25 ASN cc_start: 0.8823 (m-40) cc_final: 0.7766 (t0) REVERT: B 28 ASP cc_start: 0.8628 (m-30) cc_final: 0.8416 (m-30) REVERT: B 36 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7546 (pp) REVERT: B 75 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7998 (mm-30) REVERT: B 84 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7293 (mm) REVERT: B 254 GLU cc_start: 0.8800 (tp30) cc_final: 0.8411 (tp30) REVERT: B 385 MET cc_start: 0.8737 (ttm) cc_final: 0.8392 (ttp) REVERT: B 399 GLU cc_start: 0.8437 (pm20) cc_final: 0.8193 (pm20) REVERT: B 410 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8486 (ttmm) REVERT: B 483 MET cc_start: 0.9431 (tmm) cc_final: 0.8586 (tmm) REVERT: C 25 ASN cc_start: 0.8745 (m-40) cc_final: 0.7792 (t0) REVERT: C 36 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7646 (pp) REVERT: C 84 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7319 (mt) REVERT: C 254 GLU cc_start: 0.8871 (tp30) cc_final: 0.8505 (tp30) REVERT: C 335 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7379 (tt0) REVERT: C 410 LYS cc_start: 0.8647 (ptpp) cc_final: 0.8355 (ttmm) REVERT: C 483 MET cc_start: 0.9370 (tmm) cc_final: 0.8445 (tmm) REVERT: C 512 ARG cc_start: 0.8618 (mtp-110) cc_final: 0.8161 (mtp-110) REVERT: D 16 ASP cc_start: 0.8824 (t0) cc_final: 0.8492 (t0) REVERT: D 25 ASN cc_start: 0.8849 (m-40) cc_final: 0.7851 (t0) REVERT: D 36 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7494 (pp) REVERT: D 70 MET cc_start: 0.9041 (mtp) cc_final: 0.8780 (mtp) REVERT: D 103 GLU cc_start: 0.8838 (tp30) cc_final: 0.8298 (mm-30) REVERT: D 410 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8506 (ttmm) REVERT: D 512 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8275 (ttp80) REVERT: E 16 ASP cc_start: 0.8661 (t0) cc_final: 0.8411 (t0) REVERT: E 25 ASN cc_start: 0.8750 (m-40) cc_final: 0.7798 (t0) REVERT: E 36 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7561 (pp) REVERT: E 75 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7895 (mm-30) REVERT: E 84 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7359 (mm) REVERT: E 98 GLU cc_start: 0.8718 (pm20) cc_final: 0.8381 (mp0) REVERT: E 103 GLU cc_start: 0.8807 (tp30) cc_final: 0.7800 (mm-30) REVERT: E 256 ASP cc_start: 0.8776 (m-30) cc_final: 0.8459 (t0) REVERT: E 269 ASP cc_start: 0.8090 (m-30) cc_final: 0.7834 (m-30) REVERT: E 335 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7330 (tt0) REVERT: E 364 ASP cc_start: 0.8525 (p0) cc_final: 0.8278 (p0) REVERT: E 368 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: E 399 GLU cc_start: 0.8375 (pm20) cc_final: 0.8164 (pm20) REVERT: E 412 ARG cc_start: 0.8602 (ptp-170) cc_final: 0.8346 (ptp-170) REVERT: E 483 MET cc_start: 0.9409 (tmm) cc_final: 0.8540 (tmm) REVERT: E 487 GLU cc_start: 0.8830 (tt0) cc_final: 0.8623 (tt0) REVERT: E 512 ARG cc_start: 0.8652 (mtp-110) cc_final: 0.8257 (ttp-110) REVERT: F 16 ASP cc_start: 0.8710 (t0) cc_final: 0.8460 (t0) REVERT: F 25 ASN cc_start: 0.8856 (m-40) cc_final: 0.7913 (t0) REVERT: F 36 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7612 (pp) REVERT: F 84 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6740 (mt) REVERT: F 98 GLU cc_start: 0.8748 (pm20) cc_final: 0.8507 (pm20) REVERT: F 335 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7428 (tt0) REVERT: F 393 THR cc_start: 0.8674 (p) cc_final: 0.8441 (p) REVERT: F 399 GLU cc_start: 0.8439 (pm20) cc_final: 0.8183 (pm20) REVERT: F 417 LEU cc_start: 0.8475 (pt) cc_final: 0.8273 (pt) REVERT: F 483 MET cc_start: 0.9389 (tmm) cc_final: 0.8439 (tmm) REVERT: G 16 ASP cc_start: 0.8684 (t0) cc_final: 0.8443 (t0) REVERT: G 25 ASN cc_start: 0.8685 (m-40) cc_final: 0.7717 (t0) REVERT: G 36 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7447 (pp) REVERT: G 75 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7842 (mm-30) REVERT: G 84 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6842 (mm) REVERT: G 103 GLU cc_start: 0.8886 (tp30) cc_final: 0.8611 (mm-30) REVERT: G 105 ARG cc_start: 0.8612 (tmm160) cc_final: 0.8239 (ttp80) REVERT: G 335 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7376 (tt0) REVERT: G 399 GLU cc_start: 0.8405 (pm20) cc_final: 0.8171 (pm20) REVERT: G 410 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8450 (ttmm) REVERT: G 483 MET cc_start: 0.9473 (tmm) cc_final: 0.8497 (tmm) REVERT: G 512 ARG cc_start: 0.8606 (mtp-110) cc_final: 0.8241 (ttp80) REVERT: H 16 ASP cc_start: 0.8706 (t0) cc_final: 0.8354 (t0) REVERT: H 25 ASN cc_start: 0.8855 (m-40) cc_final: 0.7836 (t0) REVERT: H 36 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7463 (pp) REVERT: H 70 MET cc_start: 0.8989 (mtp) cc_final: 0.8664 (mtp) REVERT: H 75 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7936 (mm-30) REVERT: H 84 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6467 (mt) REVERT: H 254 GLU cc_start: 0.8911 (tp30) cc_final: 0.8683 (tp30) REVERT: H 399 GLU cc_start: 0.8423 (pm20) cc_final: 0.8169 (pm20) REVERT: H 483 MET cc_start: 0.9411 (tmm) cc_final: 0.8568 (tmm) REVERT: H 512 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8426 (ttp-110) outliers start: 62 outliers final: 44 residues processed: 541 average time/residue: 0.3259 time to fit residues: 281.1732 Evaluate side-chains 554 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 494 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 chunk 43 optimal weight: 0.0070 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.085811 restraints weight = 33429.661| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.20 r_work: 0.2756 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23376 Z= 0.177 Angle : 0.510 8.020 31640 Z= 0.256 Chirality : 0.042 0.137 3648 Planarity : 0.003 0.034 3976 Dihedral : 7.604 56.175 3724 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.61 % Allowed : 19.02 % Favored : 78.37 % 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: 2952 helix: 0.72 (0.16), residues: 1088 sheet: -1.56 (0.21), residues: 488 loop : -0.46 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 92 PHE 0.012 0.001 PHE C 401 TYR 0.009 0.001 TYR F 12 ARG 0.004 0.000 ARG H 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5705.56 seconds wall clock time: 104 minutes 9.10 seconds (6249.10 seconds total)