Starting phenix.real_space_refine on Fri Mar 15 13:01:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u23_26306/03_2024/7u23_26306.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u23_26306/03_2024/7u23_26306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u23_26306/03_2024/7u23_26306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u23_26306/03_2024/7u23_26306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u23_26306/03_2024/7u23_26306.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u23_26306/03_2024/7u23_26306.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 7375 2.51 5 N 2039 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 361": "NH1" <-> "NH2" Residue "E ARG 376": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 431": "NH1" <-> "NH2" Residue "E ARG 441": "NH1" <-> "NH2" Residue "E ARG 450": "NH1" <-> "NH2" Residue "E ARG 455": "NH1" <-> "NH2" Residue "E ARG 474": "NH1" <-> "NH2" Residue "E ARG 481": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "E TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 565": "NH1" <-> "NH2" Residue "E ARG 575": "NH1" <-> "NH2" Residue "E ARG 617": "NH1" <-> "NH2" Residue "E ARG 620": "NH1" <-> "NH2" Residue "E ARG 689": "NH1" <-> "NH2" Residue "E ARG 704": "NH1" <-> "NH2" Residue "E ARG 751": "NH1" <-> "NH2" Residue "E ARG 757": "NH1" <-> "NH2" Residue "E ARG 764": "NH1" <-> "NH2" Residue "E ARG 770": "NH1" <-> "NH2" Residue "E ARG 794": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 44": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F ARG 180": "NH1" <-> "NH2" Residue "F ARG 222": "NH1" <-> "NH2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 361": "NH1" <-> "NH2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 431": "NH1" <-> "NH2" Residue "F ARG 441": "NH1" <-> "NH2" Residue "F ARG 450": "NH1" <-> "NH2" Residue "F ARG 455": "NH1" <-> "NH2" Residue "F ARG 474": "NH1" <-> "NH2" Residue "F ARG 481": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F ARG 488": "NH1" <-> "NH2" Residue "F TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 565": "NH1" <-> "NH2" Residue "F ARG 575": "NH1" <-> "NH2" Residue "F ARG 617": "NH1" <-> "NH2" Residue "F ARG 620": "NH1" <-> "NH2" Residue "F ARG 689": "NH1" <-> "NH2" Residue "F ARG 704": "NH1" <-> "NH2" Residue "F ARG 751": "NH1" <-> "NH2" Residue "F ARG 757": "NH1" <-> "NH2" Residue "F ARG 764": "NH1" <-> "NH2" Residue "F ARG 770": "NH1" <-> "NH2" Residue "F ARG 794": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11688 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5380 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 633} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5380 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 633} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 464 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "D" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 464 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Time building chain proxies: 5.47, per 1000 atoms: 0.47 Number of scatterers: 11688 At special positions: 0 Unit cell: (107.06, 126.14, 149.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 2176 8.00 N 2039 7.00 C 7375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 22 " distance=2.03 Simple disulfide: pdb=" SG CYS E 120 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 181 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 205 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 252 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 294 " - pdb=" SG CYS E 298 " distance=2.03 Simple disulfide: pdb=" SG CYS E 302 " - pdb=" SG CYS E 323 " distance=2.03 Simple disulfide: pdb=" SG CYS E 425 " - pdb=" SG CYS E 458 " distance=2.03 Simple disulfide: pdb=" SG CYS E 776 " - pdb=" SG CYS E 785 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 22 " distance=2.03 Simple disulfide: pdb=" SG CYS F 120 " - pdb=" SG CYS F 148 " distance=2.02 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 175 " distance=2.03 Simple disulfide: pdb=" SG CYS F 162 " - pdb=" SG CYS F 181 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 189 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 205 " - pdb=" SG CYS F 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 221 " - pdb=" SG CYS F 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 234 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 252 " - pdb=" SG CYS F 273 " distance=2.03 Simple disulfide: pdb=" SG CYS F 277 " - pdb=" SG CYS F 291 " distance=2.03 Simple disulfide: pdb=" SG CYS F 294 " - pdb=" SG CYS F 298 " distance=2.03 Simple disulfide: pdb=" SG CYS F 302 " - pdb=" SG CYS F 323 " distance=2.03 Simple disulfide: pdb=" SG CYS F 425 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 785 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 47 " distance=2.04 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.7 seconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 28 sheets defined 15.6% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 65 through 69 Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 249 through 253 Processing helix chain 'E' and resid 315 through 321 removed outlier: 3.748A pdb=" N MET E 319 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 425 through 437 removed outlier: 3.783A pdb=" N ILE E 429 " --> pdb=" O CYS E 425 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 434 " --> pdb=" O TYR E 430 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL E 435 " --> pdb=" O ARG E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 701 removed outlier: 3.760A pdb=" N PHE E 701 " --> pdb=" O HIS E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 779 through 784 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 65 through 69 Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.756A pdb=" N MET F 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.533A pdb=" N GLU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 351 No H-bonds generated for 'chain 'F' and resid 349 through 351' Processing helix chain 'F' and resid 425 through 437 removed outlier: 3.865A pdb=" N ILE F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 435 " --> pdb=" O ARG F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 701 removed outlier: 3.736A pdb=" N PHE F 701 " --> pdb=" O HIS F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 782 Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.572A pdb=" N VAL C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 41 through 48 removed outlier: 3.717A pdb=" N CYS D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 61 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 10 removed outlier: 6.285A pdb=" N LEU E 29 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE E 58 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 31 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL E 60 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU E 33 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR E 85 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ARG E 112 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 87 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLU E 114 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE E 89 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE E 111 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL E 140 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE E 113 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 164 through 167 removed outlier: 3.724A pdb=" N THR E 165 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 205 through 209 removed outlier: 5.783A pdb=" N LEU E 206 " --> pdb=" O CYS E 221 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N CYS E 221 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER E 208 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 219 " --> pdb=" O SER E 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'E' and resid 245 through 248 removed outlier: 3.840A pdb=" N ARG E 245 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N CYS E 273 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG E 240 " --> pdb=" O CYS E 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AA8, first strand: chain 'E' and resid 302 through 311 removed outlier: 10.962A pdb=" N ILE E 325 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N GLU E 305 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N LYS E 327 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS E 307 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 302 through 311 removed outlier: 10.962A pdb=" N ILE E 325 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N GLU E 305 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N LYS E 327 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS E 307 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR E 417 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR E 391 " --> pdb=" O TYR E 417 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA E 419 " --> pdb=" O TYR E 391 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU E 393 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 461 through 462 removed outlier: 5.589A pdb=" N ASP E 461 " --> pdb=" O LYS E 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 465 through 470 removed outlier: 6.653A pdb=" N THR E 478 " --> pdb=" O THR E 466 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR E 468 " --> pdb=" O ILE E 476 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 476 " --> pdb=" O THR E 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 520 through 525 Processing sheet with id=AB4, first strand: chain 'E' and resid 585 through 590 removed outlier: 4.522A pdb=" N VAL E 587 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS E 600 " --> pdb=" O VAL E 587 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER E 589 " --> pdb=" O ILE E 598 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE E 598 " --> pdb=" O SER E 589 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 747 through 752 removed outlier: 4.279A pdb=" N TYR E 613 " --> pdb=" O CYS E 776 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AB7, first strand: chain 'F' and resid 6 through 10 removed outlier: 6.325A pdb=" N LEU F 29 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N PHE F 58 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE F 31 " --> pdb=" O PHE F 58 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL F 60 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU F 33 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG F 112 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL F 88 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU F 114 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE F 90 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 164 through 167 removed outlier: 3.749A pdb=" N THR F 165 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 209 removed outlier: 3.552A pdb=" N ALA F 220 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER F 208 " --> pdb=" O CYS F 218 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS F 218 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 224 through 226 Processing sheet with id=AC2, first strand: chain 'F' and resid 245 through 248 removed outlier: 3.791A pdb=" N ARG F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N CYS F 273 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG F 240 " --> pdb=" O CYS F 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=AC4, first strand: chain 'F' and resid 301 through 311 removed outlier: 11.033A pdb=" N ILE F 325 " --> pdb=" O GLU F 303 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N GLU F 305 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N LYS F 327 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS F 307 " --> pdb=" O LYS F 327 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 301 through 311 removed outlier: 11.033A pdb=" N ILE F 325 " --> pdb=" O GLU F 303 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N GLU F 305 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N LYS F 327 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS F 307 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS F 415 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 419 " --> pdb=" O VAL F 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 461 through 463 removed outlier: 5.640A pdb=" N ASP F 461 " --> pdb=" O LYS F 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 465 through 470 removed outlier: 6.622A pdb=" N THR F 478 " --> pdb=" O THR F 466 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR F 468 " --> pdb=" O ILE F 476 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE F 476 " --> pdb=" O THR F 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 520 through 525 Processing sheet with id=AC9, first strand: chain 'F' and resid 585 through 593 removed outlier: 4.511A pdb=" N VAL F 587 " --> pdb=" O LYS F 600 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS F 600 " --> pdb=" O VAL F 587 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER F 589 " --> pdb=" O ILE F 598 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE F 598 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER F 591 " --> pdb=" O GLN F 596 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN F 596 " --> pdb=" O SER F 591 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 747 through 752 removed outlier: 4.336A pdb=" N TYR F 613 " --> pdb=" O CYS F 776 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 759 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: 3.48 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3846 1.34 - 1.46: 2774 1.46 - 1.58: 5204 1.58 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 11944 Sorted by residual: bond pdb=" N SER E 579 " pdb=" CA SER E 579 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.57e+00 bond pdb=" N VAL E 580 " pdb=" CA VAL E 580 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.80e+00 bond pdb=" N THR E 576 " pdb=" CA THR E 576 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.25e-02 6.40e+03 6.45e+00 bond pdb=" N ASN E 577 " pdb=" CA ASN E 577 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.31e-02 5.83e+03 5.51e+00 bond pdb=" N ALA E 578 " pdb=" CA ALA E 578 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.28e-02 6.10e+03 3.35e+00 ... (remaining 11939 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.85: 395 106.85 - 113.65: 6629 113.65 - 120.45: 4226 120.45 - 127.25: 4816 127.25 - 134.05: 131 Bond angle restraints: 16197 Sorted by residual: angle pdb=" N ARG D 26 " pdb=" CA ARG D 26 " pdb=" C ARG D 26 " ideal model delta sigma weight residual 110.73 117.08 -6.35 1.55e+00 4.16e-01 1.68e+01 angle pdb=" CA ARG D 26 " pdb=" C ARG D 26 " pdb=" N PRO D 27 " ideal model delta sigma weight residual 117.84 121.27 -3.43 9.70e-01 1.06e+00 1.25e+01 angle pdb=" C THR E 107 " pdb=" N ARG E 108 " pdb=" CA ARG E 108 " ideal model delta sigma weight residual 122.17 117.41 4.76 1.54e+00 4.22e-01 9.56e+00 angle pdb=" CA THR E 576 " pdb=" C THR E 576 " pdb=" O THR E 576 " ideal model delta sigma weight residual 121.44 118.21 3.23 1.08e+00 8.57e-01 8.95e+00 angle pdb=" CA SER E 579 " pdb=" C SER E 579 " pdb=" O SER E 579 " ideal model delta sigma weight residual 121.66 118.31 3.35 1.22e+00 6.72e-01 7.53e+00 ... (remaining 16192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 6649 15.40 - 30.79: 479 30.79 - 46.19: 134 46.19 - 61.58: 42 61.58 - 76.98: 9 Dihedral angle restraints: 7313 sinusoidal: 3033 harmonic: 4280 Sorted by residual: dihedral pdb=" CB CYS C 7 " pdb=" SG CYS C 7 " pdb=" SG CYS C 47 " pdb=" CB CYS C 47 " ideal model delta sinusoidal sigma weight residual -86.00 -156.41 70.41 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CB CYS F 201 " pdb=" SG CYS F 201 " pdb=" SG CYS F 209 " pdb=" CB CYS F 209 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual 93.00 144.71 -51.71 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 7310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1180 0.033 - 0.067: 362 0.067 - 0.100: 169 0.100 - 0.133: 76 0.133 - 0.166: 3 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CA VAL E 580 " pdb=" N VAL E 580 " pdb=" C VAL E 580 " pdb=" CB VAL E 580 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA VAL C 24 " pdb=" N VAL C 24 " pdb=" C VAL C 24 " pdb=" CB VAL C 24 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA PRO E 422 " pdb=" N PRO E 422 " pdb=" C PRO E 422 " pdb=" CB PRO E 422 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1787 not shown) Planarity restraints: 2091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 4 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO F 5 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 5 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 5 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 143 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO F 144 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 144 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 144 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 234 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO F 235 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 235 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 235 " -0.022 5.00e-02 4.00e+02 ... (remaining 2088 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 924 2.74 - 3.28: 11587 3.28 - 3.82: 19134 3.82 - 4.36: 23678 4.36 - 4.90: 39111 Nonbonded interactions: 94434 Sorted by model distance: nonbonded pdb=" OD1 ASP E 126 " pdb=" OG SER E 128 " model vdw 2.198 2.440 nonbonded pdb=" O LYS E 503 " pdb=" OH TYR E 573 " model vdw 2.207 2.440 nonbonded pdb=" O LYS F 503 " pdb=" OH TYR F 573 " model vdw 2.209 2.440 nonbonded pdb=" O PHE E 701 " pdb=" OH TYR D 60 " model vdw 2.211 2.440 nonbonded pdb=" OD1 ASN E 698 " pdb=" N GLY D 41 " model vdw 2.234 2.520 ... (remaining 94429 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 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 256 or resid 265 through 798)) selection = (chain 'F' and (resid 1 through 624 or resid 684 through 798)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.010 Extract box with map and model: 9.730 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 28.670 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 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 : 0.004 0.045 11944 Z= 0.260 Angle : 0.592 6.353 16197 Z= 0.329 Chirality : 0.043 0.166 1790 Planarity : 0.004 0.071 2091 Dihedral : 11.885 76.976 4435 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.73 % Favored : 92.92 % Rotamer: Outliers : 2.67 % Allowed : 6.79 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1426 helix: -1.46 (0.36), residues: 153 sheet: -0.75 (0.30), residues: 289 loop : -1.56 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 79 HIS 0.004 0.001 HIS F 539 PHE 0.021 0.001 PHE F 692 TYR 0.012 0.001 TYR D 25 ARG 0.005 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 254 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ILE cc_start: 0.7420 (mt) cc_final: 0.6854 (mt) REVERT: E 100 LEU cc_start: 0.9170 (mt) cc_final: 0.8727 (mt) REVERT: E 169 ASN cc_start: 0.9159 (m-40) cc_final: 0.8858 (p0) REVERT: E 398 LEU cc_start: 0.8993 (tp) cc_final: 0.8741 (tp) REVERT: E 446 ASP cc_start: 0.6518 (m-30) cc_final: 0.6309 (m-30) REVERT: F 76 ILE cc_start: 0.9039 (mt) cc_final: 0.8718 (tt) REVERT: F 353 VAL cc_start: 0.8866 (t) cc_final: 0.8555 (t) REVERT: F 398 LEU cc_start: 0.9277 (tp) cc_final: 0.9043 (tp) REVERT: F 416 MET cc_start: 0.7559 (mtm) cc_final: 0.7232 (ptt) REVERT: F 432 MET cc_start: 0.9004 (ttt) cc_final: 0.8457 (tmm) REVERT: F 436 THR cc_start: 0.7987 (m) cc_final: 0.7439 (m) REVERT: F 448 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8813 (t0) REVERT: F 490 LEU cc_start: 0.9315 (tt) cc_final: 0.9048 (mm) REVERT: D 21 ASN cc_start: 0.7465 (m-40) cc_final: 0.7261 (p0) outliers start: 35 outliers final: 9 residues processed: 281 average time/residue: 0.2747 time to fit residues: 104.9364 Evaluate side-chains 135 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 0.0270 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 136 ASN ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 ASN E 399 GLN ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 694 ASN F 399 GLN ** F 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11944 Z= 0.248 Angle : 0.647 8.030 16197 Z= 0.347 Chirality : 0.047 0.218 1790 Planarity : 0.005 0.065 2091 Dihedral : 5.086 25.265 1610 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.75 % Favored : 93.90 % Rotamer: Outliers : 0.15 % Allowed : 2.21 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.21), residues: 1426 helix: -1.32 (0.35), residues: 170 sheet: -0.55 (0.30), residues: 292 loop : -1.41 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 402 HIS 0.004 0.001 HIS E 539 PHE 0.023 0.002 PHE E 692 TYR 0.026 0.002 TYR F 496 ARG 0.004 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 THR cc_start: 0.9060 (m) cc_final: 0.8848 (p) REVERT: E 169 ASN cc_start: 0.9188 (m-40) cc_final: 0.8784 (p0) REVERT: E 345 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8651 (tp30) REVERT: E 348 MET cc_start: 0.9197 (mpp) cc_final: 0.8989 (mpp) REVERT: E 395 ASN cc_start: 0.9172 (m110) cc_final: 0.7242 (p0) REVERT: E 398 LEU cc_start: 0.9076 (tp) cc_final: 0.8871 (tp) REVERT: F 53 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7889 (mt-10) REVERT: F 398 LEU cc_start: 0.9352 (tp) cc_final: 0.9017 (tp) REVERT: F 401 LEU cc_start: 0.9277 (mm) cc_final: 0.8774 (tp) REVERT: F 432 MET cc_start: 0.9169 (ttt) cc_final: 0.8714 (tmm) REVERT: F 436 THR cc_start: 0.8411 (m) cc_final: 0.7594 (m) REVERT: F 521 MET cc_start: 0.8124 (mmp) cc_final: 0.7873 (mmp) REVERT: F 529 ASN cc_start: 0.8852 (t0) cc_final: 0.8448 (t0) REVERT: D 21 ASN cc_start: 0.7305 (m-40) cc_final: 0.6930 (p0) outliers start: 2 outliers final: 0 residues processed: 165 average time/residue: 0.2740 time to fit residues: 62.9665 Evaluate side-chains 109 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 364 HIS E 374 ASN ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 ASN F 421 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11944 Z= 0.246 Angle : 0.615 7.435 16197 Z= 0.325 Chirality : 0.046 0.268 1790 Planarity : 0.004 0.043 2091 Dihedral : 5.140 25.863 1610 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.68 % Favored : 93.97 % Rotamer: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.21), residues: 1426 helix: -0.97 (0.37), residues: 164 sheet: -0.39 (0.30), residues: 307 loop : -1.24 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 402 HIS 0.004 0.001 HIS F 539 PHE 0.021 0.002 PHE E 692 TYR 0.024 0.002 TYR D 25 ARG 0.008 0.001 ARG E 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 169 ASN cc_start: 0.9199 (m-40) cc_final: 0.8752 (p0) REVERT: E 348 MET cc_start: 0.8960 (mpp) cc_final: 0.8627 (mpp) REVERT: E 395 ASN cc_start: 0.9030 (m110) cc_final: 0.6816 (p0) REVERT: F 53 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8206 (mt-10) REVERT: F 180 ARG cc_start: 0.8298 (mpt180) cc_final: 0.7692 (mmm160) REVERT: F 344 LEU cc_start: 0.9538 (mt) cc_final: 0.9253 (mt) REVERT: F 348 MET cc_start: 0.8348 (mpp) cc_final: 0.8020 (mpp) REVERT: F 400 GLN cc_start: 0.9356 (pm20) cc_final: 0.9095 (pm20) REVERT: F 432 MET cc_start: 0.9004 (ttt) cc_final: 0.8714 (tmm) REVERT: F 436 THR cc_start: 0.8429 (m) cc_final: 0.7308 (m) REVERT: F 521 MET cc_start: 0.8330 (mmp) cc_final: 0.8061 (mmp) REVERT: F 529 ASN cc_start: 0.8937 (t0) cc_final: 0.8501 (t0) REVERT: F 753 ASP cc_start: 0.8091 (t0) cc_final: 0.7871 (t0) REVERT: D 12 VAL cc_start: 0.9542 (m) cc_final: 0.9237 (p) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.2434 time to fit residues: 49.6740 Evaluate side-chains 96 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 14 optimal weight: 0.0870 chunk 62 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 0.0770 chunk 124 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 ASN ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11944 Z= 0.166 Angle : 0.579 8.765 16197 Z= 0.305 Chirality : 0.047 0.232 1790 Planarity : 0.004 0.044 2091 Dihedral : 5.022 23.266 1610 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1426 helix: -0.65 (0.38), residues: 163 sheet: -0.19 (0.31), residues: 298 loop : -1.19 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 402 HIS 0.006 0.001 HIS E 364 PHE 0.018 0.001 PHE E 692 TYR 0.017 0.001 TYR D 25 ARG 0.003 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 THR cc_start: 0.8977 (m) cc_final: 0.8690 (p) REVERT: E 169 ASN cc_start: 0.9205 (m-40) cc_final: 0.8752 (p0) REVERT: E 348 MET cc_start: 0.8890 (mpp) cc_final: 0.8595 (mpp) REVERT: E 395 ASN cc_start: 0.8925 (m110) cc_final: 0.8511 (m-40) REVERT: E 398 LEU cc_start: 0.8946 (tp) cc_final: 0.8687 (tp) REVERT: E 446 ASP cc_start: 0.7390 (m-30) cc_final: 0.6924 (m-30) REVERT: E 558 MET cc_start: 0.3715 (mpp) cc_final: 0.3455 (tpt) REVERT: F 53 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8081 (mt-10) REVERT: F 398 LEU cc_start: 0.9660 (mm) cc_final: 0.9316 (mm) REVERT: F 400 GLN cc_start: 0.9313 (pm20) cc_final: 0.9088 (pm20) REVERT: F 432 MET cc_start: 0.8965 (ttt) cc_final: 0.8680 (tmm) REVERT: F 436 THR cc_start: 0.8474 (m) cc_final: 0.7933 (p) REVERT: F 529 ASN cc_start: 0.8977 (t0) cc_final: 0.8459 (t0) REVERT: F 753 ASP cc_start: 0.8065 (t0) cc_final: 0.7839 (t0) REVERT: F 796 MET cc_start: 0.7194 (mmp) cc_final: 0.6991 (mmp) REVERT: D 12 VAL cc_start: 0.9505 (m) cc_final: 0.9218 (p) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2289 time to fit residues: 47.1470 Evaluate side-chains 100 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 ASN ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11944 Z= 0.199 Angle : 0.583 7.698 16197 Z= 0.305 Chirality : 0.046 0.227 1790 Planarity : 0.004 0.043 2091 Dihedral : 5.018 23.835 1610 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.75 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1426 helix: -0.50 (0.39), residues: 166 sheet: -0.15 (0.31), residues: 298 loop : -1.10 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 402 HIS 0.004 0.001 HIS F 539 PHE 0.015 0.001 PHE E 692 TYR 0.014 0.001 TYR C 60 ARG 0.008 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 THR cc_start: 0.8938 (m) cc_final: 0.8651 (p) REVERT: E 169 ASN cc_start: 0.9220 (m-40) cc_final: 0.8742 (p0) REVERT: E 348 MET cc_start: 0.8850 (mpp) cc_final: 0.8512 (mpp) REVERT: E 395 ASN cc_start: 0.8943 (m110) cc_final: 0.8560 (m-40) REVERT: E 398 LEU cc_start: 0.9087 (tp) cc_final: 0.8752 (tp) REVERT: E 404 TRP cc_start: 0.8866 (m-90) cc_final: 0.8605 (m-90) REVERT: E 446 ASP cc_start: 0.7165 (m-30) cc_final: 0.6581 (m-30) REVERT: E 521 MET cc_start: 0.2608 (mmt) cc_final: 0.1816 (mmt) REVERT: F 53 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7723 (tt0) REVERT: F 319 MET cc_start: 0.8693 (tmm) cc_final: 0.8395 (ppp) REVERT: F 398 LEU cc_start: 0.9670 (mm) cc_final: 0.9366 (mm) REVERT: F 400 GLN cc_start: 0.9358 (pm20) cc_final: 0.9124 (pm20) REVERT: F 410 THR cc_start: 0.7704 (m) cc_final: 0.7501 (m) REVERT: F 432 MET cc_start: 0.8897 (ttt) cc_final: 0.8536 (tmm) REVERT: F 436 THR cc_start: 0.8251 (m) cc_final: 0.7630 (m) REVERT: F 529 ASN cc_start: 0.8987 (t0) cc_final: 0.8456 (t0) REVERT: F 753 ASP cc_start: 0.8006 (t0) cc_final: 0.7795 (t0) REVERT: F 796 MET cc_start: 0.7318 (mmp) cc_final: 0.7092 (mmp) REVERT: D 12 VAL cc_start: 0.9527 (m) cc_final: 0.9214 (p) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2166 time to fit residues: 42.1882 Evaluate side-chains 101 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 115 optimal weight: 0.3980 chunk 64 optimal weight: 40.0000 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 ASN ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11944 Z= 0.185 Angle : 0.566 7.584 16197 Z= 0.297 Chirality : 0.046 0.325 1790 Planarity : 0.004 0.043 2091 Dihedral : 4.918 24.221 1610 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.61 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1426 helix: -0.32 (0.40), residues: 165 sheet: -0.11 (0.31), residues: 298 loop : -1.02 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 127 HIS 0.003 0.001 HIS F 539 PHE 0.015 0.001 PHE E 692 TYR 0.012 0.001 TYR F 550 ARG 0.002 0.000 ARG E 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.344 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: E 74 THR cc_start: 0.8888 (m) cc_final: 0.8592 (p) REVERT: E 169 ASN cc_start: 0.9188 (m-40) cc_final: 0.8747 (p0) REVERT: E 345 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8728 (tp30) REVERT: E 348 MET cc_start: 0.8762 (mpp) cc_final: 0.8493 (mpp) REVERT: E 395 ASN cc_start: 0.8962 (m110) cc_final: 0.8687 (m-40) REVERT: E 398 LEU cc_start: 0.9100 (tp) cc_final: 0.8721 (tp) REVERT: E 404 TRP cc_start: 0.8917 (m-90) cc_final: 0.8642 (m-90) REVERT: E 446 ASP cc_start: 0.7085 (m-30) cc_final: 0.6527 (m-30) REVERT: F 53 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7821 (tt0) REVERT: F 398 LEU cc_start: 0.9683 (mm) cc_final: 0.9383 (mm) REVERT: F 400 GLN cc_start: 0.9433 (pm20) cc_final: 0.9167 (pm20) REVERT: F 432 MET cc_start: 0.8885 (ttt) cc_final: 0.8519 (tmm) REVERT: F 436 THR cc_start: 0.8315 (m) cc_final: 0.7587 (m) REVERT: F 529 ASN cc_start: 0.9052 (t0) cc_final: 0.8509 (t0) REVERT: D 12 VAL cc_start: 0.9509 (m) cc_final: 0.9206 (p) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2017 time to fit residues: 38.7710 Evaluate side-chains 97 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0170 chunk 79 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 86 optimal weight: 0.0870 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 40.0000 chunk 85 optimal weight: 0.3980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 ASN F 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11944 Z= 0.159 Angle : 0.560 10.316 16197 Z= 0.291 Chirality : 0.046 0.250 1790 Planarity : 0.004 0.054 2091 Dihedral : 4.790 22.652 1610 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.12 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1426 helix: -0.18 (0.40), residues: 163 sheet: -0.05 (0.31), residues: 294 loop : -0.91 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 127 HIS 0.003 0.001 HIS E 364 PHE 0.012 0.001 PHE E 692 TYR 0.021 0.001 TYR D 25 ARG 0.003 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.406 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: E 74 THR cc_start: 0.8824 (m) cc_final: 0.8553 (p) REVERT: E 95 LEU cc_start: 0.9299 (tp) cc_final: 0.8601 (tp) REVERT: E 169 ASN cc_start: 0.9068 (m-40) cc_final: 0.8670 (p0) REVERT: E 345 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8694 (tp30) REVERT: E 348 MET cc_start: 0.8678 (mpp) cc_final: 0.8407 (mpp) REVERT: E 395 ASN cc_start: 0.8819 (m110) cc_final: 0.8503 (m-40) REVERT: E 398 LEU cc_start: 0.9038 (tp) cc_final: 0.8680 (tp) REVERT: E 446 ASP cc_start: 0.7003 (m-30) cc_final: 0.6429 (m-30) REVERT: F 53 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7837 (tt0) REVERT: F 331 LEU cc_start: 0.8899 (tt) cc_final: 0.8581 (mt) REVERT: F 398 LEU cc_start: 0.9665 (mm) cc_final: 0.9361 (mm) REVERT: F 400 GLN cc_start: 0.9368 (pm20) cc_final: 0.9157 (pm20) REVERT: F 402 TRP cc_start: 0.8216 (p-90) cc_final: 0.7820 (p-90) REVERT: F 409 LEU cc_start: 0.8021 (mt) cc_final: 0.7676 (tp) REVERT: F 432 MET cc_start: 0.8864 (ttt) cc_final: 0.8485 (tmm) REVERT: F 436 THR cc_start: 0.8423 (m) cc_final: 0.7473 (m) REVERT: F 529 ASN cc_start: 0.9047 (t0) cc_final: 0.8509 (t0) REVERT: F 796 MET cc_start: 0.7316 (mmp) cc_final: 0.7088 (mmp) REVERT: D 12 VAL cc_start: 0.9497 (m) cc_final: 0.9201 (p) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2018 time to fit residues: 37.3555 Evaluate side-chains 94 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 0.0010 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 0.0570 chunk 126 optimal weight: 0.9990 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11944 Z= 0.146 Angle : 0.560 8.171 16197 Z= 0.290 Chirality : 0.046 0.314 1790 Planarity : 0.004 0.089 2091 Dihedral : 4.765 21.891 1610 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.12 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1426 helix: -0.17 (0.40), residues: 165 sheet: 0.03 (0.31), residues: 294 loop : -0.87 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 404 HIS 0.003 0.001 HIS E 364 PHE 0.027 0.001 PHE E 70 TYR 0.014 0.001 TYR F 357 ARG 0.006 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 THR cc_start: 0.8826 (m) cc_final: 0.8555 (p) REVERT: E 169 ASN cc_start: 0.9059 (m-40) cc_final: 0.8663 (p0) REVERT: E 345 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8685 (tp30) REVERT: E 348 MET cc_start: 0.8613 (mpp) cc_final: 0.8379 (mpp) REVERT: E 395 ASN cc_start: 0.8753 (m110) cc_final: 0.8350 (m-40) REVERT: E 398 LEU cc_start: 0.9010 (tp) cc_final: 0.8654 (tp) REVERT: E 404 TRP cc_start: 0.8884 (m-90) cc_final: 0.8585 (m-90) REVERT: E 446 ASP cc_start: 0.6976 (m-30) cc_final: 0.6423 (m-30) REVERT: F 53 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7894 (tt0) REVERT: F 331 LEU cc_start: 0.8857 (tt) cc_final: 0.8611 (mp) REVERT: F 398 LEU cc_start: 0.9659 (mm) cc_final: 0.9337 (mm) REVERT: F 400 GLN cc_start: 0.9365 (pm20) cc_final: 0.9154 (pm20) REVERT: F 409 LEU cc_start: 0.8026 (mt) cc_final: 0.7577 (tp) REVERT: F 436 THR cc_start: 0.8380 (m) cc_final: 0.7875 (p) REVERT: F 529 ASN cc_start: 0.8988 (t0) cc_final: 0.8453 (t0) REVERT: D 12 VAL cc_start: 0.9494 (m) cc_final: 0.9217 (p) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2012 time to fit residues: 37.5407 Evaluate side-chains 93 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 0.0040 chunk 84 optimal weight: 2.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11944 Z= 0.234 Angle : 0.613 8.011 16197 Z= 0.319 Chirality : 0.047 0.266 1790 Planarity : 0.005 0.077 2091 Dihedral : 5.002 24.250 1610 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.10 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1426 helix: -0.05 (0.41), residues: 158 sheet: -0.15 (0.31), residues: 294 loop : -0.83 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 127 HIS 0.004 0.001 HIS E 697 PHE 0.022 0.002 PHE E 70 TYR 0.013 0.002 TYR E 391 ARG 0.006 0.000 ARG F 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 THR cc_start: 0.9001 (m) cc_final: 0.8705 (p) REVERT: E 92 MET cc_start: 0.7509 (ptm) cc_final: 0.6586 (tmm) REVERT: E 348 MET cc_start: 0.8595 (mpp) cc_final: 0.8300 (mpp) REVERT: E 366 LEU cc_start: 0.9181 (mt) cc_final: 0.8936 (mt) REVERT: E 395 ASN cc_start: 0.8933 (m110) cc_final: 0.8693 (m-40) REVERT: E 398 LEU cc_start: 0.9144 (tp) cc_final: 0.8908 (tp) REVERT: E 436 THR cc_start: 0.6295 (m) cc_final: 0.5881 (p) REVERT: F 53 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8199 (mm-30) REVERT: F 331 LEU cc_start: 0.8895 (tt) cc_final: 0.8572 (mt) REVERT: F 398 LEU cc_start: 0.9684 (mm) cc_final: 0.9405 (mm) REVERT: F 432 MET cc_start: 0.8731 (ppp) cc_final: 0.8459 (ppp) REVERT: F 529 ASN cc_start: 0.9069 (t0) cc_final: 0.8549 (t0) REVERT: D 12 VAL cc_start: 0.9566 (m) cc_final: 0.9234 (p) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2005 time to fit residues: 36.0829 Evaluate side-chains 84 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 143 optimal weight: 0.0980 chunk 132 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11944 Z= 0.155 Angle : 0.562 8.299 16197 Z= 0.294 Chirality : 0.046 0.273 1790 Planarity : 0.004 0.073 2091 Dihedral : 4.819 21.150 1610 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.84 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1426 helix: 0.04 (0.42), residues: 154 sheet: -0.07 (0.31), residues: 296 loop : -0.79 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 127 HIS 0.004 0.001 HIS E 364 PHE 0.019 0.001 PHE E 70 TYR 0.015 0.001 TYR F 391 ARG 0.005 0.000 ARG F 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 THR cc_start: 0.8867 (m) cc_final: 0.8571 (p) REVERT: E 92 MET cc_start: 0.7449 (ptm) cc_final: 0.6536 (tmm) REVERT: E 348 MET cc_start: 0.8547 (mpp) cc_final: 0.8245 (mpp) REVERT: E 395 ASN cc_start: 0.8825 (m110) cc_final: 0.8599 (m-40) REVERT: E 398 LEU cc_start: 0.8972 (tp) cc_final: 0.8570 (tp) REVERT: E 436 THR cc_start: 0.6029 (m) cc_final: 0.5805 (p) REVERT: E 446 ASP cc_start: 0.6901 (m-30) cc_final: 0.6325 (m-30) REVERT: F 53 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8034 (tt0) REVERT: F 319 MET cc_start: 0.8918 (ppp) cc_final: 0.8420 (ppp) REVERT: F 331 LEU cc_start: 0.8856 (tt) cc_final: 0.8595 (mp) REVERT: F 398 LEU cc_start: 0.9626 (mm) cc_final: 0.9351 (mm) REVERT: F 409 LEU cc_start: 0.8006 (mt) cc_final: 0.7581 (tp) REVERT: F 432 MET cc_start: 0.8746 (ppp) cc_final: 0.8497 (ppp) REVERT: F 529 ASN cc_start: 0.9024 (t0) cc_final: 0.8494 (t0) REVERT: D 12 VAL cc_start: 0.9541 (m) cc_final: 0.9219 (p) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1985 time to fit residues: 35.2876 Evaluate side-chains 87 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.078647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.057364 restraints weight = 85405.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.059188 restraints weight = 52310.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.060420 restraints weight = 37483.449| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11944 Z= 0.163 Angle : 0.552 8.007 16197 Z= 0.289 Chirality : 0.046 0.264 1790 Planarity : 0.004 0.066 2091 Dihedral : 4.834 20.889 1610 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.33 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1426 helix: 0.02 (0.41), residues: 160 sheet: -0.09 (0.31), residues: 300 loop : -0.77 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 404 HIS 0.003 0.001 HIS F 539 PHE 0.018 0.001 PHE E 70 TYR 0.013 0.001 TYR F 391 ARG 0.004 0.000 ARG F 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.27 seconds wall clock time: 46 minutes 30.42 seconds (2790.42 seconds total)