Starting phenix.real_space_refine on Wed Jul 24 11:33:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uts_26788/07_2024/7uts_26788.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uts_26788/07_2024/7uts_26788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uts_26788/07_2024/7uts_26788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uts_26788/07_2024/7uts_26788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uts_26788/07_2024/7uts_26788.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uts_26788/07_2024/7uts_26788.cif" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.045 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 95 5.16 5 C 16442 2.51 5 N 4406 2.21 5 O 4861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25804 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "L" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 466 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'CIS': 1, 'TRANS': 91} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 92} Unresolved non-hydrogen planarities: 92 Chain: "H" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 551 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4191 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 484} Chain breaks: 2 Chain: "B" Number of atoms: 3971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3971 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 457} Chain breaks: 6 Chain: "E" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2786 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 318} Chain breaks: 15 Chain: "I" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4108 Classifications: {'peptide': 514} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 474} Chain breaks: 4 Chain: "F" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4185 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 484} Chain breaks: 2 Chain: "C" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 985 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 9, 'TRANS': 109} Chain breaks: 7 Chain: "D" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 323 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain breaks: 5 Time building chain proxies: 13.74, per 1000 atoms: 0.53 Number of scatterers: 25804 At special positions: 0 Unit cell: (188.1, 161.7, 124.3, 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 95 16.00 O 4861 8.00 N 4406 7.00 C 16442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.04 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.03 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 494 " distance=2.04 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " 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: 9.38 Conformation dependent library (CDL) restraints added in 4.2 seconds 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6206 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 53 sheets defined 13.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'G' and resid 86 through 92 removed outlier: 4.315A pdb=" N VAL G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.607A pdb=" N MET G 190 " --> pdb=" O PRO G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 241 removed outlier: 3.837A pdb=" N VAL G 241 " --> pdb=" O PRO G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 250 Processing helix chain 'G' and resid 281 through 285 removed outlier: 3.539A pdb=" N LEU G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 385 removed outlier: 3.664A pdb=" N GLY G 385 " --> pdb=" O ARG G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 427 No H-bonds generated for 'chain 'G' and resid 425 through 427' Processing helix chain 'G' and resid 443 through 447 Processing helix chain 'G' and resid 557 through 561 Processing helix chain 'L' and resid 1 through 5 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.578A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.642A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.754A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 443 through 448 removed outlier: 4.143A pdb=" N ILE A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'B' and resid 86 through 92 removed outlier: 4.151A pdb=" N VAL B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.757A pdb=" N VAL B 241 " --> pdb=" O PRO B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.661A pdb=" N ASP B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.868A pdb=" N ASN B 560 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 removed outlier: 4.141A pdb=" N ASP E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS E 89 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 98 removed outlier: 4.423A pdb=" N ALA E 97 " --> pdb=" O GLY E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.649A pdb=" N THR E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 326 through 330 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 409 through 413 removed outlier: 4.306A pdb=" N ASP E 413 " --> pdb=" O PRO E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 562 removed outlier: 3.679A pdb=" N ASN E 560 " --> pdb=" O ASN E 557 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR E 561 " --> pdb=" O GLN E 558 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL E 562 " --> pdb=" O PHE E 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 557 through 562' Processing helix chain 'I' and resid 86 through 92 removed outlier: 3.511A pdb=" N VAL I 92 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 removed outlier: 4.663A pdb=" N ALA I 97 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP I 99 " --> pdb=" O MET I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 120 removed outlier: 3.528A pdb=" N VAL I 119 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.894A pdb=" N LEU I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 250 Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 409 through 413 removed outlier: 4.019A pdb=" N ASP I 413 " --> pdb=" O PRO I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 427 No H-bonds generated for 'chain 'I' and resid 425 through 427' Processing helix chain 'I' and resid 443 through 447 Processing helix chain 'I' and resid 557 through 562 removed outlier: 3.774A pdb=" N VAL I 562 " --> pdb=" O PHE I 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 removed outlier: 3.936A pdb=" N VAL F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 281 through 285 removed outlier: 3.513A pdb=" N LEU F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.739A pdb=" N ASP F 413 " --> pdb=" O PRO F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 427 No H-bonds generated for 'chain 'F' and resid 425 through 427' Processing helix chain 'F' and resid 443 through 447 Processing helix chain 'F' and resid 557 through 562 removed outlier: 3.902A pdb=" N VAL F 562 " --> pdb=" O PHE F 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing sheet with id=AA1, first strand: chain 'G' and resid 50 through 52 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 72 current: chain 'G' and resid 164 through 167 Processing sheet with id=AA2, first strand: chain 'G' and resid 80 through 84 Processing sheet with id=AA3, first strand: chain 'G' and resid 206 through 207 removed outlier: 4.541A pdb=" N LEU G 498 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 217 through 218 removed outlier: 4.000A pdb=" N THR G 217 " --> pdb=" O ILE G 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 277 Processing sheet with id=AA6, first strand: chain 'G' and resid 315 through 317 Processing sheet with id=AA7, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.783A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 351 through 354 removed outlier: 3.568A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 396 through 399 Processing sheet with id=AB1, first strand: chain 'G' and resid 429 through 430 Processing sheet with id=AB2, first strand: chain 'G' and resid 470 through 472 removed outlier: 6.809A pdb=" N ASP G 471 " --> pdb=" O CYS G 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.475A pdb=" N UNK H 85 " --> pdb=" O UNK H 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 72 current: chain 'A' and resid 164 through 167 Processing sheet with id=AB7, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AB8, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AB9, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AC1, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.831A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 351 through 354 Processing sheet with id=AC3, first strand: chain 'A' and resid 396 through 399 Processing sheet with id=AC4, first strand: chain 'A' and resid 463 through 464 removed outlier: 4.357A pdb=" N TYR A 464 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 574 " --> pdb=" O TYR A 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 470 through 472 removed outlier: 6.797A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 44 through 45 current: chain 'C' and resid 105 through 111 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 72 current: chain 'B' and resid 164 through 167 Processing sheet with id=AC8, first strand: chain 'B' and resid 80 through 84 Processing sheet with id=AC9, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AD1, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AD2, first strand: chain 'B' and resid 335 through 336 removed outlier: 6.498A pdb=" N GLU B 335 " --> pdb=" O ALA B 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 345 through 348 Processing sheet with id=AD4, first strand: chain 'B' and resid 377 through 378 removed outlier: 3.558A pdb=" N PHE B 398 " --> pdb=" O TYR B 378 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 435 through 436 removed outlier: 5.727A pdb=" N ILE B 442 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD7, first strand: chain 'E' and resid 49 through 50 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 71 current: chain 'E' and resid 164 through 166 Processing sheet with id=AD8, first strand: chain 'E' and resid 206 through 210 removed outlier: 7.050A pdb=" N THR E 206 " --> pdb=" O TRP E 109 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TRP E 109 " --> pdb=" O THR E 206 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP E 208 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU E 498 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AE1, first strand: chain 'I' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 58 through 72 current: chain 'I' and resid 164 through 168 Processing sheet with id=AE2, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AE3, first strand: chain 'I' and resid 215 through 218 removed outlier: 3.640A pdb=" N GLY I 235 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR I 217 " --> pdb=" O TYR I 233 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR I 233 " --> pdb=" O THR I 217 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 276 through 277 Processing sheet with id=AE5, first strand: chain 'I' and resid 335 through 336 removed outlier: 6.209A pdb=" N GLU I 335 " --> pdb=" O ALA I 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 345 through 346 Processing sheet with id=AE7, first strand: chain 'I' and resid 377 through 380 Processing sheet with id=AE8, first strand: chain 'I' and resid 415 through 416 Processing sheet with id=AE9, first strand: chain 'F' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 72 current: chain 'F' and resid 166 through 167 Processing sheet with id=AF1, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AF2, first strand: chain 'F' and resid 216 through 218 Processing sheet with id=AF3, first strand: chain 'F' and resid 276 through 277 Processing sheet with id=AF4, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.731A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 463 through 464 removed outlier: 3.768A pdb=" N TYR F 464 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 470 through 472 removed outlier: 6.867A pdb=" N ASP F 471 " --> pdb=" O CYS F 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 69 through 72 removed outlier: 4.191A pdb=" N TRP C 528 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN C 147 " --> pdb=" O TRP C 528 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 68 through 73 removed outlier: 5.184A pdb=" N THR D 523 " --> pdb=" O MET D 73 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 615 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: 7.72 Time building geometry restraints manager: 10.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8075 1.34 - 1.46: 6375 1.46 - 1.58: 11897 1.58 - 1.71: 3 1.71 - 1.83: 169 Bond restraints: 26519 Sorted by residual: bond pdb=" C LEU G 578 " pdb=" N ALA G 579 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.06e+01 bond pdb=" C ALA B 503 " pdb=" N PRO B 504 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.66e+00 bond pdb=" CB TRP A 120 " pdb=" CG TRP A 120 " ideal model delta sigma weight residual 1.498 1.408 0.090 3.10e-02 1.04e+03 8.40e+00 bond pdb=" N GLY C 496 " pdb=" CA GLY C 496 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.76e+00 bond pdb=" N GLY I 37 " pdb=" CA GLY I 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 ... (remaining 26514 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.59: 1151 106.59 - 113.48: 13824 113.48 - 120.37: 9948 120.37 - 127.26: 10850 127.26 - 134.15: 478 Bond angle restraints: 36251 Sorted by residual: angle pdb=" N GLY F 286 " pdb=" CA GLY F 286 " pdb=" C GLY F 286 " ideal model delta sigma weight residual 111.56 116.78 -5.22 1.01e+00 9.80e-01 2.67e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 110.43 116.00 -5.57 1.35e+00 5.49e-01 1.70e+01 angle pdb=" N GLY F 320 " pdb=" CA GLY F 320 " pdb=" C GLY F 320 " ideal model delta sigma weight residual 113.99 119.25 -5.26 1.28e+00 6.10e-01 1.69e+01 angle pdb=" CA UNK L 58 " pdb=" C UNK L 58 " pdb=" N UNK L 59 " ideal model delta sigma weight residual 116.20 124.28 -8.08 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N GLY I 320 " pdb=" CA GLY I 320 " pdb=" C GLY I 320 " ideal model delta sigma weight residual 113.86 119.66 -5.80 1.50e+00 4.44e-01 1.50e+01 ... (remaining 36246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14476 17.99 - 35.99: 855 35.99 - 53.98: 128 53.98 - 71.98: 43 71.98 - 89.97: 33 Dihedral angle restraints: 15535 sinusoidal: 5954 harmonic: 9581 Sorted by residual: dihedral pdb=" CA ASP B 100 " pdb=" C ASP B 100 " pdb=" N ILE B 101 " pdb=" CA ILE B 101 " ideal model delta harmonic sigma weight residual -180.00 -147.67 -32.33 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N LEU A 422 " pdb=" CA LEU A 422 " ideal model delta harmonic sigma weight residual 180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA TYR G 233 " pdb=" C TYR G 233 " pdb=" N HIS G 234 " pdb=" CA HIS G 234 " ideal model delta harmonic sigma weight residual 180.00 -150.37 -29.63 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 15532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2375 0.042 - 0.084: 1125 0.084 - 0.126: 352 0.126 - 0.168: 109 0.168 - 0.210: 12 Chirality restraints: 3973 Sorted by residual: chirality pdb=" CA ILE C 204 " pdb=" N ILE C 204 " pdb=" C ILE C 204 " pdb=" CB ILE C 204 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE C 145 " pdb=" N ILE C 145 " pdb=" C ILE C 145 " pdb=" CB ILE C 145 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE F 219 " pdb=" N ILE F 219 " pdb=" C ILE F 219 " pdb=" CB ILE F 219 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 3970 not shown) Planarity restraints: 4735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.09e+01 pdb=" NE ARG A 408 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 107 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO B 108 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 216 " 0.240 9.50e-02 1.11e+02 1.08e-01 7.16e+00 pdb=" NE ARG G 216 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G 216 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 216 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 216 " 0.010 2.00e-02 2.50e+03 ... (remaining 4732 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7518 2.82 - 3.34: 23984 3.34 - 3.86: 42817 3.86 - 4.38: 50900 4.38 - 4.90: 85398 Nonbonded interactions: 210617 Sorted by model distance: nonbonded pdb=" OH TYR B 343 " pdb=" OD1 ASN I 321 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASN G 443 " pdb=" OG1 THR G 445 " model vdw 2.334 2.440 nonbonded pdb=" OG SER A 348 " pdb=" N THR A 349 " model vdw 2.354 2.520 nonbonded pdb=" N ASP B 239 " pdb=" OD1 ASP B 239 " model vdw 2.370 2.520 nonbonded pdb=" O LEU F 128 " pdb=" OG1 THR F 132 " model vdw 2.391 2.440 ... (remaining 210612 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' and (resid 45 through 153 or resid 165 through 251 or resid 254 throu \ gh 291 or resid 305 through 356 or resid 376 through 404 or resid 408 through 45 \ 6 or resid 461 through 473 or resid 479 through 490 or resid 494 through 581)) selection = (chain 'B' and (resid 45 through 153 or resid 165 through 356 or resid 376 throu \ gh 404 or resid 408 through 456 or resid 461 through 581)) selection = (chain 'F' and (resid 45 through 251 or resid 254 through 291 or resid 305 throu \ gh 356 or resid 376 through 404 or resid 408 through 456 or resid 461 through 47 \ 3 or resid 479 through 490 or resid 494 through 581)) selection = (chain 'G' and (resid 45 through 153 or resid 165 through 251 or resid 254 throu \ gh 291 or resid 305 through 356 or resid 376 through 404 or resid 408 through 45 \ 6 or resid 461 through 473 or resid 479 through 490 or resid 494 through 581)) selection = (chain 'I' and (resid 45 through 153 or resid 165 through 251 or resid 254 throu \ gh 291 or resid 305 through 356 or resid 376 through 473 or resid 479 through 49 \ 0 or resid 494 through 581)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 64.770 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 26519 Z= 0.555 Angle : 0.966 8.184 36251 Z= 0.527 Chirality : 0.054 0.210 3973 Planarity : 0.007 0.132 4735 Dihedral : 13.015 89.974 9314 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.99 % Allowed : 5.13 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 2990 helix: -1.98 (0.38), residues: 112 sheet: -0.69 (0.18), residues: 705 loop : -0.66 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 545 HIS 0.008 0.002 HIS A 137 PHE 0.043 0.003 PHE A 448 TYR 0.032 0.003 TYR G 524 ARG 0.008 0.001 ARG G 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 834 time to evaluate : 2.813 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: G 50 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7280 (mt-10) REVERT: G 59 VAL cc_start: 0.8861 (t) cc_final: 0.8342 (m) REVERT: G 60 GLU cc_start: 0.7127 (tt0) cc_final: 0.6836 (tt0) REVERT: G 125 ASP cc_start: 0.6855 (m-30) cc_final: 0.6470 (m-30) REVERT: G 135 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6767 (mt-10) REVERT: G 174 MET cc_start: 0.7432 (mtp) cc_final: 0.7215 (mtp) REVERT: G 177 LEU cc_start: 0.7952 (tp) cc_final: 0.7721 (tp) REVERT: G 197 PHE cc_start: 0.7761 (m-10) cc_final: 0.7412 (m-80) REVERT: G 198 TYR cc_start: 0.8411 (m-80) cc_final: 0.8194 (m-10) REVERT: G 271 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7733 (mtpp) REVERT: G 330 ILE cc_start: 0.8187 (tp) cc_final: 0.7910 (tp) REVERT: G 382 ARG cc_start: 0.6031 (mtm180) cc_final: 0.5719 (mtm180) REVERT: G 387 LYS cc_start: 0.8382 (ttpp) cc_final: 0.7696 (ttmm) REVERT: G 397 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7961 (mtm180) REVERT: G 492 ASN cc_start: 0.7956 (m-40) cc_final: 0.7650 (m-40) REVERT: G 536 LYS cc_start: 0.8305 (ttpp) cc_final: 0.7851 (ttpp) REVERT: G 559 PHE cc_start: 0.8285 (m-80) cc_final: 0.7537 (m-80) REVERT: G 569 MET cc_start: 0.7257 (mmm) cc_final: 0.7052 (mmm) REVERT: G 570 LYS cc_start: 0.7967 (ptpt) cc_final: 0.7583 (ptpt) REVERT: A 56 ASN cc_start: 0.7626 (m110) cc_final: 0.7382 (m110) REVERT: A 99 ASP cc_start: 0.6934 (t70) cc_final: 0.6278 (t70) REVERT: A 100 ASP cc_start: 0.7145 (m-30) cc_final: 0.6556 (m-30) REVERT: A 109 TRP cc_start: 0.8297 (m100) cc_final: 0.7861 (m100) REVERT: A 142 GLU cc_start: 0.7504 (pt0) cc_final: 0.7192 (pt0) REVERT: A 174 MET cc_start: 0.7025 (mtp) cc_final: 0.6417 (mtp) REVERT: A 183 MET cc_start: 0.7201 (mmm) cc_final: 0.6671 (mmm) REVERT: A 192 SER cc_start: 0.7582 (t) cc_final: 0.7274 (t) REVERT: A 211 TYR cc_start: 0.7393 (m-80) cc_final: 0.7085 (m-10) REVERT: A 218 LEU cc_start: 0.8598 (tp) cc_final: 0.8284 (tt) REVERT: A 219 ILE cc_start: 0.8567 (mm) cc_final: 0.8327 (mm) REVERT: A 274 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7525 (mmm-85) REVERT: A 303 PHE cc_start: 0.7997 (m-80) cc_final: 0.7602 (m-80) REVERT: A 306 ILE cc_start: 0.8607 (tp) cc_final: 0.8313 (tt) REVERT: A 415 ILE cc_start: 0.8387 (mm) cc_final: 0.8186 (mm) REVERT: A 436 ILE cc_start: 0.9015 (pt) cc_final: 0.8657 (mt) REVERT: A 458 ASN cc_start: 0.8002 (m110) cc_final: 0.7794 (m110) REVERT: A 471 ASP cc_start: 0.7069 (t0) cc_final: 0.6301 (t0) REVERT: A 530 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6651 (ttpp) REVERT: A 533 LEU cc_start: 0.8315 (tp) cc_final: 0.8112 (tp) REVERT: A 543 HIS cc_start: 0.6915 (m170) cc_final: 0.6655 (m170) REVERT: A 553 ILE cc_start: 0.8641 (tt) cc_final: 0.8305 (tt) REVERT: A 559 PHE cc_start: 0.8444 (m-80) cc_final: 0.8172 (m-10) REVERT: A 570 LYS cc_start: 0.7968 (ptpt) cc_final: 0.7700 (ptpt) REVERT: A 575 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7979 (mtpt) REVERT: A 582 LYS cc_start: 0.8237 (ttpp) cc_final: 0.8036 (ttpp) REVERT: B 93 ASN cc_start: 0.8055 (m110) cc_final: 0.7328 (p0) REVERT: B 101 ILE cc_start: 0.7832 (pt) cc_final: 0.7597 (pt) REVERT: B 104 GLN cc_start: 0.7991 (pt0) cc_final: 0.7394 (pt0) REVERT: B 117 TRP cc_start: 0.7119 (m100) cc_final: 0.6219 (m100) REVERT: B 125 ASP cc_start: 0.8160 (m-30) cc_final: 0.7798 (m-30) REVERT: B 126 TRP cc_start: 0.7614 (t-100) cc_final: 0.7389 (t-100) REVERT: B 128 LEU cc_start: 0.9183 (tp) cc_final: 0.8964 (tp) REVERT: B 134 SER cc_start: 0.7612 (p) cc_final: 0.7241 (p) REVERT: B 135 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 143 GLN cc_start: 0.7531 (mt0) cc_final: 0.7137 (mt0) REVERT: B 150 LEU cc_start: 0.8494 (tp) cc_final: 0.8084 (tp) REVERT: B 151 LYS cc_start: 0.8193 (mttm) cc_final: 0.7920 (mttm) REVERT: B 173 LEU cc_start: 0.8157 (tp) cc_final: 0.7946 (tp) REVERT: B 174 MET cc_start: 0.6648 (mtp) cc_final: 0.6329 (mtp) REVERT: B 183 MET cc_start: 0.6823 (mmm) cc_final: 0.6227 (mmm) REVERT: B 190 MET cc_start: 0.7626 (tpp) cc_final: 0.7207 (tpp) REVERT: B 198 TYR cc_start: 0.6764 (m-80) cc_final: 0.6188 (m-80) REVERT: B 209 ARG cc_start: 0.7748 (pmt170) cc_final: 0.7548 (pmt170) REVERT: B 266 PHE cc_start: 0.7027 (t80) cc_final: 0.6355 (t80) REVERT: B 268 PHE cc_start: 0.7315 (m-80) cc_final: 0.6727 (m-80) REVERT: B 382 ARG cc_start: 0.7435 (mmt90) cc_final: 0.7172 (mmt-90) REVERT: B 469 ILE cc_start: 0.8066 (mt) cc_final: 0.7544 (mt) REVERT: B 470 TRP cc_start: 0.7994 (p90) cc_final: 0.7790 (p90) REVERT: B 471 ASP cc_start: 0.5225 (t0) cc_final: 0.4899 (t0) REVERT: B 498 LEU cc_start: 0.8508 (tp) cc_final: 0.8307 (tp) REVERT: B 499 PHE cc_start: 0.8449 (m-80) cc_final: 0.8159 (m-80) REVERT: B 501 LYS cc_start: 0.7774 (tttt) cc_final: 0.7126 (tttt) REVERT: B 509 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6339 (mm-30) REVERT: B 527 PHE cc_start: 0.7067 (p90) cc_final: 0.6554 (p90) REVERT: B 532 LYS cc_start: 0.7309 (tttm) cc_final: 0.7000 (tttm) REVERT: B 533 LEU cc_start: 0.7769 (tp) cc_final: 0.7408 (tp) REVERT: B 536 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7743 (ttpp) REVERT: B 551 MET cc_start: 0.5557 (mmt) cc_final: 0.5213 (mmt) REVERT: E 45 PHE cc_start: 0.7397 (t80) cc_final: 0.6847 (t80) REVERT: E 87 MET cc_start: 0.7129 (ttt) cc_final: 0.6884 (ttt) REVERT: E 129 ILE cc_start: 0.8958 (mt) cc_final: 0.8725 (mt) REVERT: E 143 GLN cc_start: 0.7550 (mt0) cc_final: 0.7080 (mt0) REVERT: E 166 ASN cc_start: 0.6737 (m110) cc_final: 0.6522 (m110) REVERT: E 190 MET cc_start: 0.5520 (mtm) cc_final: 0.5176 (mtm) REVERT: E 329 THR cc_start: 0.4936 (t) cc_final: 0.4472 (m) REVERT: E 331 MET cc_start: 0.7202 (pmm) cc_final: 0.6934 (pmm) REVERT: E 377 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6247 (mtp180) REVERT: E 378 TYR cc_start: 0.6998 (m-80) cc_final: 0.6391 (m-80) REVERT: E 398 PHE cc_start: 0.7596 (p90) cc_final: 0.7299 (p90) REVERT: E 400 TYR cc_start: 0.7661 (t80) cc_final: 0.7443 (t80) REVERT: E 527 PHE cc_start: 0.7359 (p90) cc_final: 0.7082 (p90) REVERT: E 549 GLN cc_start: 0.7850 (tt0) cc_final: 0.6976 (tt0) REVERT: E 561 TYR cc_start: 0.8188 (m-80) cc_final: 0.7455 (m-80) REVERT: I 47 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7704 (t0) REVERT: I 52 LYS cc_start: 0.7339 (ttmm) cc_final: 0.7060 (ttmm) REVERT: I 60 GLU cc_start: 0.7188 (tt0) cc_final: 0.6904 (tt0) REVERT: I 87 MET cc_start: 0.6075 (ttp) cc_final: 0.5696 (ttp) REVERT: I 115 ASN cc_start: 0.7611 (t0) cc_final: 0.7351 (t0) REVERT: I 143 GLN cc_start: 0.8195 (mt0) cc_final: 0.7916 (mt0) REVERT: I 144 GLU cc_start: 0.7244 (pt0) cc_final: 0.6939 (pt0) REVERT: I 147 ASN cc_start: 0.8063 (t0) cc_final: 0.7303 (t0) REVERT: I 174 MET cc_start: 0.7030 (mtp) cc_final: 0.6634 (mtp) REVERT: I 201 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7951 (mtpt) REVERT: I 261 PHE cc_start: 0.7863 (t80) cc_final: 0.7459 (t80) REVERT: I 268 PHE cc_start: 0.7657 (m-80) cc_final: 0.7120 (m-80) REVERT: I 273 CYS cc_start: 0.7447 (t) cc_final: 0.7156 (t) REVERT: I 331 MET cc_start: 0.7165 (ttm) cc_final: 0.6940 (ttm) REVERT: I 387 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8112 (ttmm) REVERT: I 427 ASP cc_start: 0.8315 (m-30) cc_final: 0.7944 (m-30) REVERT: I 444 TYR cc_start: 0.8120 (p90) cc_final: 0.7790 (p90) REVERT: I 468 GLN cc_start: 0.6753 (mm110) cc_final: 0.6518 (mm110) REVERT: I 518 MET cc_start: 0.6677 (ptp) cc_final: 0.6177 (ptp) REVERT: I 532 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7551 (ttpp) REVERT: I 538 LYS cc_start: 0.8163 (tttp) cc_final: 0.7868 (ttmm) REVERT: I 539 LEU cc_start: 0.8624 (mt) cc_final: 0.8346 (mp) REVERT: I 543 HIS cc_start: 0.7176 (m170) cc_final: 0.6971 (m170) REVERT: I 544 THR cc_start: 0.7971 (p) cc_final: 0.7483 (p) REVERT: I 546 ASN cc_start: 0.8032 (p0) cc_final: 0.7708 (p0) REVERT: I 550 GLN cc_start: 0.7970 (mt0) cc_final: 0.7685 (mt0) REVERT: I 551 MET cc_start: 0.6694 (tmm) cc_final: 0.5495 (tmm) REVERT: I 558 GLN cc_start: 0.8140 (tt0) cc_final: 0.7881 (tt0) REVERT: I 559 PHE cc_start: 0.7862 (m-80) cc_final: 0.7648 (m-10) REVERT: I 573 TYR cc_start: 0.8200 (p90) cc_final: 0.7668 (p90) REVERT: I 574 GLU cc_start: 0.7427 (tp30) cc_final: 0.6914 (tp30) REVERT: I 575 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7881 (mtmm) REVERT: I 581 ARG cc_start: 0.6875 (ttm170) cc_final: 0.6309 (ttm170) REVERT: F 51 PHE cc_start: 0.6676 (m-80) cc_final: 0.6286 (m-80) REVERT: F 52 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7363 (ttmm) REVERT: F 53 PHE cc_start: 0.7263 (m-80) cc_final: 0.7059 (m-80) REVERT: F 54 LEU cc_start: 0.8225 (mt) cc_final: 0.7989 (mt) REVERT: F 59 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.7743 (m) REVERT: F 60 GLU cc_start: 0.7612 (tt0) cc_final: 0.7131 (tt0) REVERT: F 96 MET cc_start: 0.7373 (mpp) cc_final: 0.7130 (mpp) REVERT: F 143 GLN cc_start: 0.7348 (mp10) cc_final: 0.6786 (mp10) REVERT: F 180 ASN cc_start: 0.7703 (t0) cc_final: 0.7355 (t0) REVERT: F 218 LEU cc_start: 0.8221 (mt) cc_final: 0.7955 (mp) REVERT: F 232 ILE cc_start: 0.7414 (mt) cc_final: 0.6988 (mt) REVERT: F 243 PHE cc_start: 0.7766 (t80) cc_final: 0.7539 (t80) REVERT: F 244 TYR cc_start: 0.7522 (m-80) cc_final: 0.7282 (m-10) REVERT: F 266 PHE cc_start: 0.7586 (t80) cc_final: 0.7314 (t80) REVERT: F 271 LYS cc_start: 0.8256 (mtpp) cc_final: 0.8009 (mtpp) REVERT: F 282 ASN cc_start: 0.8164 (m110) cc_final: 0.7907 (m-40) REVERT: F 283 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7689 (tpp80) REVERT: F 338 TYR cc_start: 0.8382 (p90) cc_final: 0.8181 (p90) REVERT: F 404 GLN cc_start: 0.3889 (OUTLIER) cc_final: 0.3193 (tm-30) REVERT: F 405 ASP cc_start: 0.6062 (m-30) cc_final: 0.5676 (m-30) REVERT: F 430 LEU cc_start: 0.8341 (tp) cc_final: 0.8100 (tt) REVERT: F 431 LEU cc_start: 0.8489 (mt) cc_final: 0.8275 (mp) REVERT: F 450 THR cc_start: 0.8716 (p) cc_final: 0.8415 (t) REVERT: F 475 ASP cc_start: 0.7314 (t0) cc_final: 0.6731 (t0) REVERT: F 484 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8306 (m) REVERT: F 485 ASN cc_start: 0.7779 (p0) cc_final: 0.7402 (p0) REVERT: F 489 VAL cc_start: 0.8130 (m) cc_final: 0.7871 (m) REVERT: F 493 ASN cc_start: 0.8088 (m110) cc_final: 0.7855 (m-40) REVERT: F 538 LYS cc_start: 0.7563 (tptp) cc_final: 0.6704 (tppt) REVERT: F 551 MET cc_start: 0.6510 (ttt) cc_final: 0.6053 (ttt) REVERT: C 174 MET cc_start: 0.7001 (mtp) cc_final: 0.6320 (mtp) outliers start: 27 outliers final: 10 residues processed: 842 average time/residue: 0.4230 time to fit residues: 545.6306 Evaluate side-chains 813 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 799 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 484 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 3.9990 chunk 246 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 84 optimal weight: 40.0000 chunk 166 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 295 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN G 417 ASN ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 GLN G 497 GLN A 403 HIS B 127 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 508 ASN B 558 GLN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 26519 Z= 0.291 Angle : 0.622 8.517 36251 Z= 0.320 Chirality : 0.044 0.157 3973 Planarity : 0.005 0.053 4735 Dihedral : 6.738 64.939 3523 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.97 % Allowed : 10.04 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.82 (0.14), residues: 2990 helix: -0.92 (0.45), residues: 111 sheet: -0.50 (0.18), residues: 756 loop : -0.51 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 545 HIS 0.008 0.001 HIS B 137 PHE 0.026 0.002 PHE B 398 TYR 0.020 0.002 TYR F 233 ARG 0.009 0.001 ARG F 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 785 time to evaluate : 2.792 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: G 59 VAL cc_start: 0.8758 (t) cc_final: 0.8361 (m) REVERT: G 60 GLU cc_start: 0.7183 (tt0) cc_final: 0.6971 (tt0) REVERT: G 80 ARG cc_start: 0.7646 (mtm180) cc_final: 0.7445 (mtm-85) REVERT: G 85 ASN cc_start: 0.7691 (t0) cc_final: 0.6595 (t0) REVERT: G 101 ILE cc_start: 0.8538 (mt) cc_final: 0.7688 (mt) REVERT: G 125 ASP cc_start: 0.6710 (m-30) cc_final: 0.6340 (m-30) REVERT: G 174 MET cc_start: 0.7443 (mtp) cc_final: 0.7220 (mtp) REVERT: G 211 TYR cc_start: 0.8155 (m-80) cc_final: 0.7423 (m-80) REVERT: G 248 ASN cc_start: 0.7814 (t0) cc_final: 0.7606 (t0) REVERT: G 263 THR cc_start: 0.8001 (m) cc_final: 0.7606 (p) REVERT: G 271 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7682 (mtpp) REVERT: G 338 TYR cc_start: 0.8652 (p90) cc_final: 0.8425 (p90) REVERT: G 382 ARG cc_start: 0.6049 (mtm180) cc_final: 0.5573 (mtm180) REVERT: G 458 ASN cc_start: 0.7455 (m-40) cc_final: 0.7168 (m110) REVERT: G 468 GLN cc_start: 0.7881 (mt0) cc_final: 0.7620 (mt0) REVERT: G 492 ASN cc_start: 0.7885 (m-40) cc_final: 0.7635 (m-40) REVERT: G 497 GLN cc_start: 0.8246 (mt0) cc_final: 0.7952 (mt0) REVERT: G 536 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7954 (ttpp) REVERT: G 559 PHE cc_start: 0.8097 (m-80) cc_final: 0.7447 (m-80) REVERT: G 560 ASN cc_start: 0.7845 (m-40) cc_final: 0.7506 (m-40) REVERT: A 56 ASN cc_start: 0.7553 (m110) cc_final: 0.7331 (m110) REVERT: A 98 LEU cc_start: 0.7750 (mt) cc_final: 0.7003 (mt) REVERT: A 100 ASP cc_start: 0.7063 (m-30) cc_final: 0.6523 (m-30) REVERT: A 109 TRP cc_start: 0.8335 (m100) cc_final: 0.7722 (m100) REVERT: A 174 MET cc_start: 0.7085 (mtp) cc_final: 0.6283 (mtp) REVERT: A 183 MET cc_start: 0.7162 (mmm) cc_final: 0.6573 (mmm) REVERT: A 211 TYR cc_start: 0.7243 (m-80) cc_final: 0.6973 (m-80) REVERT: A 218 LEU cc_start: 0.8426 (tp) cc_final: 0.8084 (tt) REVERT: A 219 ILE cc_start: 0.8666 (mm) cc_final: 0.8436 (mm) REVERT: A 265 THR cc_start: 0.7938 (p) cc_final: 0.7537 (p) REVERT: A 350 GLN cc_start: 0.7133 (mt0) cc_final: 0.6818 (mt0) REVERT: A 411 GLU cc_start: 0.7566 (mp0) cc_final: 0.7125 (mp0) REVERT: A 458 ASN cc_start: 0.8003 (m110) cc_final: 0.7696 (m110) REVERT: A 530 LYS cc_start: 0.7145 (ttmt) cc_final: 0.6764 (ttpp) REVERT: A 533 LEU cc_start: 0.8426 (tp) cc_final: 0.8217 (tp) REVERT: A 543 HIS cc_start: 0.6893 (m170) cc_final: 0.6544 (m170) REVERT: A 570 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7736 (ptpt) REVERT: A 575 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7618 (mtpt) REVERT: B 80 ARG cc_start: 0.7239 (mtt-85) cc_final: 0.6723 (mtt-85) REVERT: B 101 ILE cc_start: 0.8189 (pt) cc_final: 0.7900 (pt) REVERT: B 104 GLN cc_start: 0.7938 (pt0) cc_final: 0.7653 (pt0) REVERT: B 125 ASP cc_start: 0.7951 (m-30) cc_final: 0.7551 (m-30) REVERT: B 135 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7117 (mt-10) REVERT: B 145 ILE cc_start: 0.8259 (mt) cc_final: 0.7807 (mm) REVERT: B 150 LEU cc_start: 0.8368 (tp) cc_final: 0.8022 (tp) REVERT: B 173 LEU cc_start: 0.8106 (tp) cc_final: 0.7897 (tp) REVERT: B 174 MET cc_start: 0.6607 (mtp) cc_final: 0.6285 (mtp) REVERT: B 178 ASP cc_start: 0.5558 (t0) cc_final: 0.5357 (t0) REVERT: B 183 MET cc_start: 0.6720 (mmm) cc_final: 0.6222 (mmm) REVERT: B 190 MET cc_start: 0.7848 (tpp) cc_final: 0.7425 (tpp) REVERT: B 198 TYR cc_start: 0.7099 (m-80) cc_final: 0.6699 (m-80) REVERT: B 247 GLU cc_start: 0.6226 (mp0) cc_final: 0.5962 (mp0) REVERT: B 266 PHE cc_start: 0.7008 (t80) cc_final: 0.6567 (t80) REVERT: B 377 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6404 (mmm-85) REVERT: B 382 ARG cc_start: 0.7393 (mmt90) cc_final: 0.7126 (mmt-90) REVERT: B 383 GLN cc_start: 0.7710 (tp-100) cc_final: 0.7188 (tm-30) REVERT: B 469 ILE cc_start: 0.7955 (mt) cc_final: 0.7452 (mt) REVERT: B 470 TRP cc_start: 0.8093 (p90) cc_final: 0.7791 (p90) REVERT: B 499 PHE cc_start: 0.8439 (m-80) cc_final: 0.7720 (m-80) REVERT: B 501 LYS cc_start: 0.7718 (tttt) cc_final: 0.7110 (tttt) REVERT: B 508 ASN cc_start: 0.8390 (t0) cc_final: 0.8157 (t0) REVERT: B 509 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6362 (mm-30) REVERT: B 527 PHE cc_start: 0.7035 (p90) cc_final: 0.6574 (p90) REVERT: B 530 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8209 (ttmt) REVERT: B 532 LYS cc_start: 0.7405 (tttm) cc_final: 0.7081 (tttm) REVERT: B 533 LEU cc_start: 0.7762 (tp) cc_final: 0.7378 (tp) REVERT: B 536 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7812 (ttpp) REVERT: B 551 MET cc_start: 0.5746 (mmt) cc_final: 0.5229 (mmt) REVERT: E 45 PHE cc_start: 0.7420 (t80) cc_final: 0.6856 (t80) REVERT: E 127 GLN cc_start: 0.7458 (mp10) cc_final: 0.5586 (tp40) REVERT: E 129 ILE cc_start: 0.8846 (mt) cc_final: 0.8587 (mt) REVERT: E 145 ILE cc_start: 0.8305 (mt) cc_final: 0.7791 (mt) REVERT: E 166 ASN cc_start: 0.6900 (m110) cc_final: 0.6662 (m110) REVERT: E 190 MET cc_start: 0.5474 (mtm) cc_final: 0.5149 (mtm) REVERT: E 377 ARG cc_start: 0.6683 (mtm-85) cc_final: 0.6051 (mtm-85) REVERT: E 378 TYR cc_start: 0.6968 (m-80) cc_final: 0.6296 (m-80) REVERT: E 398 PHE cc_start: 0.7839 (p90) cc_final: 0.7510 (p90) REVERT: E 400 TYR cc_start: 0.7763 (t80) cc_final: 0.7481 (t80) REVERT: E 527 PHE cc_start: 0.7329 (p90) cc_final: 0.6957 (p90) REVERT: E 529 TRP cc_start: 0.7814 (t60) cc_final: 0.7549 (t60) REVERT: E 530 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7498 (tmtt) REVERT: E 551 MET cc_start: 0.6589 (ttt) cc_final: 0.6341 (ttt) REVERT: E 561 TYR cc_start: 0.8245 (m-80) cc_final: 0.7442 (m-80) REVERT: E 565 ASN cc_start: 0.8292 (m-40) cc_final: 0.7420 (t0) REVERT: E 566 ILE cc_start: 0.8304 (pt) cc_final: 0.8002 (pt) REVERT: I 47 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7310 (t0) REVERT: I 52 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7411 (ttmm) REVERT: I 55 GLU cc_start: 0.7160 (tt0) cc_final: 0.6904 (tt0) REVERT: I 60 GLU cc_start: 0.7362 (tt0) cc_final: 0.7035 (tt0) REVERT: I 87 MET cc_start: 0.6249 (ttp) cc_final: 0.5689 (ttp) REVERT: I 115 ASN cc_start: 0.7707 (t0) cc_final: 0.6913 (t0) REVERT: I 143 GLN cc_start: 0.8128 (mt0) cc_final: 0.7866 (mt0) REVERT: I 144 GLU cc_start: 0.7243 (pt0) cc_final: 0.6929 (pt0) REVERT: I 174 MET cc_start: 0.7010 (mtp) cc_final: 0.6600 (mtp) REVERT: I 193 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: I 261 PHE cc_start: 0.7903 (t80) cc_final: 0.7537 (t80) REVERT: I 268 PHE cc_start: 0.7707 (m-80) cc_final: 0.7204 (m-80) REVERT: I 273 CYS cc_start: 0.7401 (t) cc_final: 0.7090 (t) REVERT: I 319 MET cc_start: 0.7246 (tpt) cc_final: 0.6900 (tpp) REVERT: I 331 MET cc_start: 0.7276 (ttm) cc_final: 0.7057 (ttm) REVERT: I 387 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8097 (ttmm) REVERT: I 396 GLU cc_start: 0.7654 (tt0) cc_final: 0.7379 (tt0) REVERT: I 427 ASP cc_start: 0.8282 (m-30) cc_final: 0.8068 (m-30) REVERT: I 518 MET cc_start: 0.6719 (ptp) cc_final: 0.6283 (ptp) REVERT: I 538 LYS cc_start: 0.7958 (tttp) cc_final: 0.7555 (ttmm) REVERT: I 543 HIS cc_start: 0.7060 (m170) cc_final: 0.6843 (m170) REVERT: I 544 THR cc_start: 0.7883 (p) cc_final: 0.7324 (p) REVERT: I 546 ASN cc_start: 0.7911 (p0) cc_final: 0.7603 (p0) REVERT: I 551 MET cc_start: 0.6675 (tmm) cc_final: 0.5594 (tmm) REVERT: I 573 TYR cc_start: 0.8270 (p90) cc_final: 0.7705 (p90) REVERT: I 575 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7786 (mtmm) REVERT: F 52 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7314 (ttmm) REVERT: F 59 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7763 (p) REVERT: F 60 GLU cc_start: 0.7556 (tt0) cc_final: 0.7131 (tt0) REVERT: F 96 MET cc_start: 0.7478 (mpp) cc_final: 0.7131 (mpp) REVERT: F 101 ILE cc_start: 0.8314 (mm) cc_final: 0.7976 (mm) REVERT: F 143 GLN cc_start: 0.7265 (mp10) cc_final: 0.6755 (mp10) REVERT: F 180 ASN cc_start: 0.7671 (t0) cc_final: 0.7335 (t0) REVERT: F 213 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7399 (tm-30) REVERT: F 242 GLN cc_start: 0.7273 (mt0) cc_final: 0.6912 (mt0) REVERT: F 243 PHE cc_start: 0.7899 (t80) cc_final: 0.7556 (t80) REVERT: F 244 TYR cc_start: 0.7158 (m-80) cc_final: 0.6383 (m-80) REVERT: F 248 ASN cc_start: 0.7134 (m-40) cc_final: 0.6804 (t0) REVERT: F 271 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7981 (mtpp) REVERT: F 282 ASN cc_start: 0.7998 (m110) cc_final: 0.7737 (m-40) REVERT: F 283 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7784 (tpt-90) REVERT: F 311 ASP cc_start: 0.7116 (p0) cc_final: 0.6795 (p0) REVERT: F 335 GLU cc_start: 0.6806 (tt0) cc_final: 0.6521 (tt0) REVERT: F 404 GLN cc_start: 0.3820 (OUTLIER) cc_final: 0.2582 (tt0) REVERT: F 408 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7526 (mmt-90) REVERT: F 416 GLN cc_start: 0.8498 (pt0) cc_final: 0.8295 (pt0) REVERT: F 431 LEU cc_start: 0.8400 (mt) cc_final: 0.8179 (mp) REVERT: F 450 THR cc_start: 0.8712 (p) cc_final: 0.8478 (t) REVERT: F 475 ASP cc_start: 0.7358 (t0) cc_final: 0.6689 (t0) REVERT: F 489 VAL cc_start: 0.8203 (m) cc_final: 0.7994 (m) REVERT: F 551 MET cc_start: 0.6464 (ttt) cc_final: 0.5908 (ttt) REVERT: C 174 MET cc_start: 0.7097 (mtp) cc_final: 0.6436 (mtp) REVERT: C 236 THR cc_start: 0.4734 (OUTLIER) cc_final: 0.4164 (p) outliers start: 81 outliers final: 49 residues processed: 806 average time/residue: 0.3869 time to fit residues: 477.0794 Evaluate side-chains 818 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 762 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 491 GLN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 193 GLU Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 164 optimal weight: 40.0000 chunk 91 optimal weight: 30.0000 chunk 245 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 319 optimal weight: 20.0000 chunk 263 optimal weight: 30.0000 chunk 293 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN G 386 GLN G 505 ASN G 577 GLN B 127 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN F 318 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 26519 Z= 0.385 Angle : 0.630 8.382 36251 Z= 0.323 Chirality : 0.045 0.191 3973 Planarity : 0.005 0.050 4735 Dihedral : 6.318 64.570 3518 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.41 % Allowed : 12.31 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.76 (0.14), residues: 2990 helix: -0.49 (0.48), residues: 106 sheet: -0.53 (0.18), residues: 741 loop : -0.47 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 545 HIS 0.007 0.001 HIS B 137 PHE 0.029 0.002 PHE I 146 TYR 0.026 0.002 TYR G 524 ARG 0.010 0.001 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 785 time to evaluate : 2.705 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: G 59 VAL cc_start: 0.8765 (t) cc_final: 0.8391 (m) REVERT: G 60 GLU cc_start: 0.7103 (tt0) cc_final: 0.6870 (tt0) REVERT: G 125 ASP cc_start: 0.6740 (m-30) cc_final: 0.6412 (m-30) REVERT: G 174 MET cc_start: 0.7429 (mtp) cc_final: 0.7208 (mtp) REVERT: G 197 PHE cc_start: 0.7951 (m-80) cc_final: 0.7624 (m-80) REVERT: G 211 TYR cc_start: 0.8173 (m-80) cc_final: 0.7422 (m-80) REVERT: G 239 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6697 (m-30) REVERT: G 271 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7731 (mtpp) REVERT: G 338 TYR cc_start: 0.8695 (p90) cc_final: 0.8463 (p90) REVERT: G 380 PHE cc_start: 0.8007 (p90) cc_final: 0.7728 (p90) REVERT: G 382 ARG cc_start: 0.5692 (mtm180) cc_final: 0.5203 (mtm180) REVERT: G 492 ASN cc_start: 0.7868 (m-40) cc_final: 0.7534 (m-40) REVERT: G 497 GLN cc_start: 0.8199 (mt0) cc_final: 0.7943 (mt0) REVERT: G 536 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7819 (ttpp) REVERT: G 559 PHE cc_start: 0.8110 (m-80) cc_final: 0.7404 (m-80) REVERT: G 560 ASN cc_start: 0.7808 (m-40) cc_final: 0.7424 (m-40) REVERT: A 56 ASN cc_start: 0.7577 (m110) cc_final: 0.7338 (m110) REVERT: A 98 LEU cc_start: 0.7768 (mt) cc_final: 0.7056 (mt) REVERT: A 100 ASP cc_start: 0.7087 (m-30) cc_final: 0.6467 (m-30) REVERT: A 174 MET cc_start: 0.7155 (mtp) cc_final: 0.6827 (mtp) REVERT: A 183 MET cc_start: 0.7127 (mmm) cc_final: 0.6492 (mmm) REVERT: A 211 TYR cc_start: 0.7279 (m-80) cc_final: 0.6965 (m-80) REVERT: A 216 ARG cc_start: 0.6704 (ttt90) cc_final: 0.6001 (ttt90) REVERT: A 218 LEU cc_start: 0.8386 (tp) cc_final: 0.8059 (tt) REVERT: A 265 THR cc_start: 0.7932 (p) cc_final: 0.7626 (p) REVERT: A 344 SER cc_start: 0.8118 (t) cc_final: 0.7619 (p) REVERT: A 346 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7030 (mp0) REVERT: A 436 ILE cc_start: 0.9054 (pt) cc_final: 0.8580 (mt) REVERT: A 458 ASN cc_start: 0.7982 (m110) cc_final: 0.7690 (m110) REVERT: A 473 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7383 (tm-30) REVERT: A 530 LYS cc_start: 0.7255 (ttmt) cc_final: 0.6891 (ttpp) REVERT: A 533 LEU cc_start: 0.8486 (tp) cc_final: 0.8276 (tp) REVERT: A 543 HIS cc_start: 0.6841 (m170) cc_final: 0.6586 (m170) REVERT: A 570 LYS cc_start: 0.7871 (ptpt) cc_final: 0.7622 (ptpt) REVERT: A 574 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6596 (mm-30) REVERT: A 575 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7770 (mtpt) REVERT: B 80 ARG cc_start: 0.7218 (mtt-85) cc_final: 0.6583 (mtt-85) REVERT: B 101 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7845 (pt) REVERT: B 145 ILE cc_start: 0.8225 (mt) cc_final: 0.7791 (mm) REVERT: B 150 LEU cc_start: 0.8371 (tp) cc_final: 0.8061 (tp) REVERT: B 174 MET cc_start: 0.6636 (mtp) cc_final: 0.6316 (mtp) REVERT: B 183 MET cc_start: 0.6774 (mmm) cc_final: 0.6267 (mmm) REVERT: B 190 MET cc_start: 0.7836 (tpp) cc_final: 0.7417 (tpp) REVERT: B 198 TYR cc_start: 0.7026 (m-80) cc_final: 0.6488 (m-80) REVERT: B 237 ASP cc_start: 0.7159 (m-30) cc_final: 0.6807 (m-30) REVERT: B 247 GLU cc_start: 0.6238 (mp0) cc_final: 0.5557 (mp0) REVERT: B 382 ARG cc_start: 0.7521 (mmt90) cc_final: 0.7157 (mmp80) REVERT: B 383 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7078 (tm-30) REVERT: B 469 ILE cc_start: 0.7930 (mt) cc_final: 0.7306 (mt) REVERT: B 470 TRP cc_start: 0.8122 (p90) cc_final: 0.7854 (p90) REVERT: B 499 PHE cc_start: 0.8398 (m-80) cc_final: 0.7763 (m-80) REVERT: B 501 LYS cc_start: 0.7817 (tttt) cc_final: 0.7252 (tttt) REVERT: B 509 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6391 (mm-30) REVERT: B 527 PHE cc_start: 0.7113 (p90) cc_final: 0.6535 (p90) REVERT: B 530 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8162 (ttmt) REVERT: B 532 LYS cc_start: 0.7448 (tttm) cc_final: 0.7155 (tttm) REVERT: B 533 LEU cc_start: 0.7742 (tp) cc_final: 0.7394 (tp) REVERT: B 551 MET cc_start: 0.5840 (mmt) cc_final: 0.5321 (mmt) REVERT: B 553 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5706 (mt) REVERT: E 45 PHE cc_start: 0.7420 (t80) cc_final: 0.6866 (t80) REVERT: E 46 ASN cc_start: 0.7442 (t0) cc_final: 0.7233 (t0) REVERT: E 127 GLN cc_start: 0.7234 (mp10) cc_final: 0.5478 (tp40) REVERT: E 166 ASN cc_start: 0.7008 (m110) cc_final: 0.6777 (m110) REVERT: E 190 MET cc_start: 0.5528 (mtm) cc_final: 0.5169 (mtm) REVERT: E 274 ARG cc_start: 0.6813 (ttt-90) cc_final: 0.6371 (ttt-90) REVERT: E 329 THR cc_start: 0.4865 (t) cc_final: 0.4477 (m) REVERT: E 378 TYR cc_start: 0.7020 (m-80) cc_final: 0.6350 (m-80) REVERT: E 398 PHE cc_start: 0.7766 (p90) cc_final: 0.7422 (p90) REVERT: E 400 TYR cc_start: 0.7762 (t80) cc_final: 0.7478 (t80) REVERT: E 527 PHE cc_start: 0.7282 (p90) cc_final: 0.6997 (p90) REVERT: E 561 TYR cc_start: 0.8263 (m-80) cc_final: 0.7403 (m-80) REVERT: E 565 ASN cc_start: 0.8353 (m-40) cc_final: 0.7347 (t0) REVERT: I 47 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7373 (t0) REVERT: I 52 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7395 (ttmm) REVERT: I 53 PHE cc_start: 0.7913 (m-80) cc_final: 0.7620 (m-80) REVERT: I 60 GLU cc_start: 0.7387 (tt0) cc_final: 0.7033 (tt0) REVERT: I 87 MET cc_start: 0.6289 (ttp) cc_final: 0.5846 (ttp) REVERT: I 101 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8035 (pp) REVERT: I 115 ASN cc_start: 0.7625 (t0) cc_final: 0.6901 (t0) REVERT: I 144 GLU cc_start: 0.7279 (pt0) cc_final: 0.6955 (pt0) REVERT: I 174 MET cc_start: 0.7043 (mtp) cc_final: 0.6547 (mtp) REVERT: I 193 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7004 (mt-10) REVERT: I 268 PHE cc_start: 0.7707 (m-80) cc_final: 0.7285 (m-80) REVERT: I 273 CYS cc_start: 0.7451 (t) cc_final: 0.7204 (t) REVERT: I 319 MET cc_start: 0.7099 (tpt) cc_final: 0.6868 (tpp) REVERT: I 331 MET cc_start: 0.7275 (ttm) cc_final: 0.7046 (ttm) REVERT: I 386 GLN cc_start: 0.8182 (tt0) cc_final: 0.7942 (tt0) REVERT: I 387 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8127 (ttmm) REVERT: I 396 GLU cc_start: 0.7623 (tt0) cc_final: 0.7177 (tt0) REVERT: I 427 ASP cc_start: 0.8335 (m-30) cc_final: 0.8127 (m-30) REVERT: I 535 PHE cc_start: 0.8331 (m-80) cc_final: 0.7825 (m-80) REVERT: I 538 LYS cc_start: 0.8049 (tttp) cc_final: 0.7798 (ttmm) REVERT: I 544 THR cc_start: 0.7882 (p) cc_final: 0.7344 (p) REVERT: I 546 ASN cc_start: 0.7913 (p0) cc_final: 0.7618 (p0) REVERT: I 550 GLN cc_start: 0.7838 (mt0) cc_final: 0.7417 (mm110) REVERT: I 551 MET cc_start: 0.6580 (tmm) cc_final: 0.4998 (tmm) REVERT: I 573 TYR cc_start: 0.8358 (p90) cc_final: 0.7853 (p90) REVERT: I 574 GLU cc_start: 0.7282 (tp30) cc_final: 0.6859 (tt0) REVERT: I 575 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7772 (mtmm) REVERT: F 52 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7470 (ttmm) REVERT: F 60 GLU cc_start: 0.7634 (tt0) cc_final: 0.7221 (tt0) REVERT: F 101 ILE cc_start: 0.8345 (mm) cc_final: 0.7966 (mm) REVERT: F 143 GLN cc_start: 0.7323 (mp10) cc_final: 0.6764 (mp10) REVERT: F 180 ASN cc_start: 0.7697 (t0) cc_final: 0.7340 (t0) REVERT: F 213 GLN cc_start: 0.7525 (tm-30) cc_final: 0.7265 (tm-30) REVERT: F 243 PHE cc_start: 0.7987 (t80) cc_final: 0.7568 (t80) REVERT: F 248 ASN cc_start: 0.7195 (m-40) cc_final: 0.6834 (t0) REVERT: F 266 PHE cc_start: 0.7899 (t80) cc_final: 0.7528 (t80) REVERT: F 271 LYS cc_start: 0.8289 (mtpp) cc_final: 0.8004 (mtpp) REVERT: F 280 GLN cc_start: 0.7909 (mm110) cc_final: 0.7517 (mm110) REVERT: F 283 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7740 (tpt-90) REVERT: F 311 ASP cc_start: 0.7133 (p0) cc_final: 0.6660 (p0) REVERT: F 312 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8171 (ptpp) REVERT: F 327 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6822 (mm-30) REVERT: F 335 GLU cc_start: 0.7036 (tt0) cc_final: 0.6785 (tt0) REVERT: F 404 GLN cc_start: 0.3843 (OUTLIER) cc_final: 0.2812 (tt0) REVERT: F 475 ASP cc_start: 0.7314 (t0) cc_final: 0.6603 (t0) REVERT: F 489 VAL cc_start: 0.8241 (m) cc_final: 0.8029 (m) REVERT: F 545 TRP cc_start: 0.8063 (t-100) cc_final: 0.7782 (t-100) REVERT: F 551 MET cc_start: 0.6443 (ttt) cc_final: 0.5915 (ttt) REVERT: F 569 MET cc_start: 0.5699 (mmm) cc_final: 0.5486 (mmm) REVERT: C 174 MET cc_start: 0.7191 (mtp) cc_final: 0.6595 (mtp) outliers start: 93 outliers final: 63 residues processed: 818 average time/residue: 0.4015 time to fit residues: 504.4278 Evaluate side-chains 833 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 763 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 443 ASN Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 490 CYS Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 292 optimal weight: 30.0000 chunk 222 optimal weight: 7.9990 chunk 153 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 296 optimal weight: 0.1980 chunk 314 optimal weight: 7.9990 chunk 155 optimal weight: 40.0000 chunk 281 optimal weight: 4.9990 chunk 84 optimal weight: 40.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 GLN G 577 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN A 546 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN F 282 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 26519 Z= 0.343 Angle : 0.610 10.673 36251 Z= 0.310 Chirality : 0.044 0.196 3973 Planarity : 0.005 0.048 4735 Dihedral : 5.956 65.474 3512 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.40 % Allowed : 13.74 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.70 (0.15), residues: 2990 helix: -0.20 (0.50), residues: 100 sheet: -0.49 (0.18), residues: 760 loop : -0.43 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 528 HIS 0.007 0.001 HIS B 137 PHE 0.030 0.002 PHE B 398 TYR 0.028 0.002 TYR B 464 ARG 0.011 0.001 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 760 time to evaluate : 2.692 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: G 59 VAL cc_start: 0.8729 (t) cc_final: 0.8337 (m) REVERT: G 60 GLU cc_start: 0.7093 (tt0) cc_final: 0.6880 (tt0) REVERT: G 125 ASP cc_start: 0.6741 (m-30) cc_final: 0.6408 (m-30) REVERT: G 135 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6907 (mt-10) REVERT: G 142 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6509 (mm-30) REVERT: G 143 GLN cc_start: 0.7954 (mt0) cc_final: 0.7739 (mt0) REVERT: G 174 MET cc_start: 0.7401 (mtp) cc_final: 0.7174 (mtp) REVERT: G 197 PHE cc_start: 0.8007 (m-80) cc_final: 0.7765 (m-80) REVERT: G 211 TYR cc_start: 0.8156 (m-80) cc_final: 0.7744 (m-80) REVERT: G 217 THR cc_start: 0.7895 (p) cc_final: 0.7584 (p) REVERT: G 239 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: G 248 ASN cc_start: 0.7837 (t0) cc_final: 0.7596 (t0) REVERT: G 271 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7747 (mtpp) REVERT: G 338 TYR cc_start: 0.8695 (p90) cc_final: 0.8449 (p90) REVERT: G 350 GLN cc_start: 0.7189 (mt0) cc_final: 0.6976 (mt0) REVERT: G 382 ARG cc_start: 0.5667 (mtm180) cc_final: 0.5272 (mtm180) REVERT: G 536 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7817 (ttpp) REVERT: G 559 PHE cc_start: 0.8033 (m-80) cc_final: 0.7382 (m-80) REVERT: G 560 ASN cc_start: 0.7806 (m-40) cc_final: 0.7420 (m-40) REVERT: A 56 ASN cc_start: 0.7517 (m110) cc_final: 0.7298 (m110) REVERT: A 98 LEU cc_start: 0.7679 (mt) cc_final: 0.6968 (mt) REVERT: A 100 ASP cc_start: 0.6944 (m-30) cc_final: 0.6369 (m-30) REVERT: A 174 MET cc_start: 0.7150 (mtp) cc_final: 0.6779 (mtp) REVERT: A 183 MET cc_start: 0.7099 (mmm) cc_final: 0.6483 (mmm) REVERT: A 211 TYR cc_start: 0.7270 (m-80) cc_final: 0.6948 (m-80) REVERT: A 218 LEU cc_start: 0.8332 (tp) cc_final: 0.8027 (tt) REVERT: A 265 THR cc_start: 0.7947 (p) cc_final: 0.7653 (p) REVERT: A 344 SER cc_start: 0.8054 (t) cc_final: 0.7626 (p) REVERT: A 346 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6983 (mp0) REVERT: A 403 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.6891 (m-70) REVERT: A 433 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7975 (p) REVERT: A 530 LYS cc_start: 0.7296 (ttmt) cc_final: 0.6854 (ttpp) REVERT: A 533 LEU cc_start: 0.8493 (tp) cc_final: 0.8264 (tp) REVERT: A 543 HIS cc_start: 0.6859 (m170) cc_final: 0.6620 (m170) REVERT: A 570 LYS cc_start: 0.7875 (ptpt) cc_final: 0.7555 (ptpt) REVERT: A 574 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6418 (mm-30) REVERT: A 575 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7764 (mtpt) REVERT: B 80 ARG cc_start: 0.7185 (mtt-85) cc_final: 0.6516 (mtt-85) REVERT: B 96 MET cc_start: 0.7215 (mtm) cc_final: 0.7014 (mtm) REVERT: B 101 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7924 (pt) REVERT: B 142 GLU cc_start: 0.7679 (pt0) cc_final: 0.7172 (pt0) REVERT: B 145 ILE cc_start: 0.8197 (mt) cc_final: 0.7794 (mm) REVERT: B 150 LEU cc_start: 0.8319 (tp) cc_final: 0.8050 (tp) REVERT: B 174 MET cc_start: 0.6816 (mtp) cc_final: 0.6390 (mtp) REVERT: B 183 MET cc_start: 0.6762 (mmm) cc_final: 0.6252 (mmm) REVERT: B 190 MET cc_start: 0.7827 (tpp) cc_final: 0.7409 (tpp) REVERT: B 198 TYR cc_start: 0.6945 (m-80) cc_final: 0.6443 (m-80) REVERT: B 237 ASP cc_start: 0.7273 (m-30) cc_final: 0.6795 (m-30) REVERT: B 266 PHE cc_start: 0.7153 (t80) cc_final: 0.6646 (t80) REVERT: B 306 ILE cc_start: 0.7805 (mp) cc_final: 0.7600 (pt) REVERT: B 342 TYR cc_start: 0.7321 (p90) cc_final: 0.7091 (p90) REVERT: B 377 ARG cc_start: 0.6115 (tpp80) cc_final: 0.5099 (tpp80) REVERT: B 382 ARG cc_start: 0.7585 (mmt90) cc_final: 0.7043 (mmp80) REVERT: B 383 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7111 (tm-30) REVERT: B 469 ILE cc_start: 0.8011 (mt) cc_final: 0.7585 (mp) REVERT: B 470 TRP cc_start: 0.8182 (p90) cc_final: 0.7891 (p90) REVERT: B 501 LYS cc_start: 0.7750 (tttt) cc_final: 0.7233 (tttt) REVERT: B 509 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6360 (mm-30) REVERT: B 527 PHE cc_start: 0.7032 (p90) cc_final: 0.6482 (p90) REVERT: B 530 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8109 (ttmt) REVERT: B 532 LYS cc_start: 0.7496 (tttm) cc_final: 0.7204 (tttm) REVERT: B 533 LEU cc_start: 0.7733 (tp) cc_final: 0.7361 (tp) REVERT: B 536 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7774 (ttpp) REVERT: B 551 MET cc_start: 0.5939 (mmt) cc_final: 0.5445 (mmt) REVERT: E 45 PHE cc_start: 0.7384 (t80) cc_final: 0.6835 (t80) REVERT: E 46 ASN cc_start: 0.7482 (t0) cc_final: 0.7227 (t0) REVERT: E 85 ASN cc_start: 0.6551 (OUTLIER) cc_final: 0.6186 (p0) REVERT: E 87 MET cc_start: 0.7437 (ttt) cc_final: 0.6969 (ttt) REVERT: E 127 GLN cc_start: 0.7204 (mp10) cc_final: 0.6878 (tp40) REVERT: E 166 ASN cc_start: 0.6937 (m110) cc_final: 0.6723 (m110) REVERT: E 190 MET cc_start: 0.5543 (mtm) cc_final: 0.5171 (mtm) REVERT: E 378 TYR cc_start: 0.7037 (m-80) cc_final: 0.6348 (m-80) REVERT: E 398 PHE cc_start: 0.7822 (p90) cc_final: 0.7448 (p90) REVERT: E 400 TYR cc_start: 0.7753 (t80) cc_final: 0.7462 (t80) REVERT: E 527 PHE cc_start: 0.7292 (p90) cc_final: 0.6965 (p90) REVERT: E 561 TYR cc_start: 0.8290 (m-80) cc_final: 0.7549 (m-80) REVERT: E 565 ASN cc_start: 0.8354 (m-40) cc_final: 0.7336 (t0) REVERT: E 566 ILE cc_start: 0.8314 (pt) cc_final: 0.8019 (pt) REVERT: I 47 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7305 (t0) REVERT: I 52 LYS cc_start: 0.7730 (ttmm) cc_final: 0.7427 (ttmm) REVERT: I 53 PHE cc_start: 0.7944 (m-80) cc_final: 0.7645 (m-80) REVERT: I 60 GLU cc_start: 0.7386 (tt0) cc_final: 0.7039 (tt0) REVERT: I 87 MET cc_start: 0.6478 (ttp) cc_final: 0.6040 (ttp) REVERT: I 115 ASN cc_start: 0.7612 (t0) cc_final: 0.6999 (t0) REVERT: I 144 GLU cc_start: 0.7233 (pt0) cc_final: 0.6897 (pt0) REVERT: I 174 MET cc_start: 0.7096 (mtp) cc_final: 0.6642 (mtp) REVERT: I 193 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7049 (mt-10) REVERT: I 201 LYS cc_start: 0.8273 (mtpt) cc_final: 0.8040 (ttpt) REVERT: I 268 PHE cc_start: 0.7732 (m-80) cc_final: 0.7320 (m-80) REVERT: I 273 CYS cc_start: 0.7528 (t) cc_final: 0.7306 (t) REVERT: I 319 MET cc_start: 0.6751 (tpt) cc_final: 0.6405 (tpp) REVERT: I 331 MET cc_start: 0.7286 (ttm) cc_final: 0.7048 (ttm) REVERT: I 386 GLN cc_start: 0.8182 (tt0) cc_final: 0.7956 (tt0) REVERT: I 387 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8165 (ttmm) REVERT: I 396 GLU cc_start: 0.7573 (tt0) cc_final: 0.7114 (tt0) REVERT: I 427 ASP cc_start: 0.8322 (m-30) cc_final: 0.8122 (m-30) REVERT: I 444 TYR cc_start: 0.7547 (p90) cc_final: 0.7225 (p90) REVERT: I 535 PHE cc_start: 0.8364 (m-80) cc_final: 0.7854 (m-80) REVERT: I 538 LYS cc_start: 0.8077 (tttp) cc_final: 0.7821 (ttmm) REVERT: I 544 THR cc_start: 0.7887 (p) cc_final: 0.7188 (t) REVERT: I 546 ASN cc_start: 0.7923 (p0) cc_final: 0.7414 (p0) REVERT: I 573 TYR cc_start: 0.8256 (p90) cc_final: 0.7765 (p90) REVERT: I 575 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7720 (mtmm) REVERT: I 576 SER cc_start: 0.7926 (t) cc_final: 0.7640 (p) REVERT: F 52 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7479 (ttmm) REVERT: F 60 GLU cc_start: 0.7620 (tt0) cc_final: 0.7217 (tt0) REVERT: F 96 MET cc_start: 0.7596 (mpp) cc_final: 0.7115 (mpp) REVERT: F 101 ILE cc_start: 0.8301 (mm) cc_final: 0.7948 (mm) REVERT: F 143 GLN cc_start: 0.7358 (mp10) cc_final: 0.6764 (mp10) REVERT: F 180 ASN cc_start: 0.7702 (t0) cc_final: 0.7330 (t0) REVERT: F 213 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7259 (tm-30) REVERT: F 248 ASN cc_start: 0.7230 (m-40) cc_final: 0.6793 (t0) REVERT: F 266 PHE cc_start: 0.7846 (t80) cc_final: 0.7500 (t80) REVERT: F 271 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8051 (mtpp) REVERT: F 280 GLN cc_start: 0.7970 (mm110) cc_final: 0.7518 (mm-40) REVERT: F 311 ASP cc_start: 0.7098 (p0) cc_final: 0.6697 (p0) REVERT: F 312 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8033 (ptpp) REVERT: F 327 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6807 (mm-30) REVERT: F 350 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: F 425 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8162 (p) REVERT: F 475 ASP cc_start: 0.7238 (t0) cc_final: 0.6518 (t0) REVERT: F 484 VAL cc_start: 0.8500 (m) cc_final: 0.8076 (p) REVERT: F 538 LYS cc_start: 0.7717 (tppt) cc_final: 0.7171 (tppt) REVERT: F 545 TRP cc_start: 0.8041 (t-100) cc_final: 0.7826 (t-100) REVERT: F 551 MET cc_start: 0.6370 (ttt) cc_final: 0.5866 (ttt) REVERT: F 569 MET cc_start: 0.5720 (mmm) cc_final: 0.5462 (mmm) REVERT: C 174 MET cc_start: 0.7267 (mtp) cc_final: 0.6798 (mtp) outliers start: 120 outliers final: 86 residues processed: 803 average time/residue: 0.3870 time to fit residues: 477.4828 Evaluate side-chains 839 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 743 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 524 TYR Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain G residue 570 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 443 ASN Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 577 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 490 CYS Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 261 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 160 optimal weight: 0.5980 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN A 115 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN F 282 ASN F 491 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 26519 Z= 0.265 Angle : 0.580 9.912 36251 Z= 0.293 Chirality : 0.043 0.178 3973 Planarity : 0.005 0.049 4735 Dihedral : 5.596 65.925 3509 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.88 % Allowed : 15.02 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.59 (0.15), residues: 2990 helix: -0.15 (0.51), residues: 100 sheet: -0.42 (0.18), residues: 771 loop : -0.36 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 528 HIS 0.006 0.001 HIS B 137 PHE 0.025 0.002 PHE B 398 TYR 0.029 0.002 TYR G 464 ARG 0.011 0.000 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 763 time to evaluate : 2.389 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: G 59 VAL cc_start: 0.8721 (t) cc_final: 0.8329 (m) REVERT: G 60 GLU cc_start: 0.7026 (tt0) cc_final: 0.6797 (tt0) REVERT: G 125 ASP cc_start: 0.6697 (m-30) cc_final: 0.6380 (m-30) REVERT: G 135 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6919 (mt-10) REVERT: G 142 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6414 (mm-30) REVERT: G 174 MET cc_start: 0.7392 (mtp) cc_final: 0.7162 (mtp) REVERT: G 197 PHE cc_start: 0.8012 (m-10) cc_final: 0.7787 (m-80) REVERT: G 211 TYR cc_start: 0.8170 (m-80) cc_final: 0.7776 (m-80) REVERT: G 217 THR cc_start: 0.7825 (p) cc_final: 0.7468 (p) REVERT: G 239 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: G 248 ASN cc_start: 0.7789 (t0) cc_final: 0.7575 (t0) REVERT: G 265 THR cc_start: 0.7982 (m) cc_final: 0.7632 (m) REVERT: G 271 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7746 (mtpp) REVERT: G 350 GLN cc_start: 0.7162 (mt0) cc_final: 0.6925 (mt0) REVERT: G 382 ARG cc_start: 0.5625 (mtm180) cc_final: 0.5103 (mtm180) REVERT: G 390 THR cc_start: 0.8697 (t) cc_final: 0.8409 (p) REVERT: G 409 TYR cc_start: 0.7947 (t80) cc_final: 0.7627 (t80) REVERT: G 536 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7802 (ttpp) REVERT: G 559 PHE cc_start: 0.7997 (m-80) cc_final: 0.7351 (m-80) REVERT: G 560 ASN cc_start: 0.7815 (m-40) cc_final: 0.7399 (m-40) REVERT: G 581 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7735 (ttp-110) REVERT: A 56 ASN cc_start: 0.7460 (m110) cc_final: 0.7230 (m110) REVERT: A 66 SER cc_start: 0.7645 (m) cc_final: 0.7110 (m) REVERT: A 98 LEU cc_start: 0.7674 (mt) cc_final: 0.6991 (mt) REVERT: A 100 ASP cc_start: 0.6851 (m-30) cc_final: 0.6316 (m-30) REVERT: A 174 MET cc_start: 0.7216 (mtp) cc_final: 0.6818 (mtp) REVERT: A 183 MET cc_start: 0.7105 (mmm) cc_final: 0.6493 (mmm) REVERT: A 211 TYR cc_start: 0.7263 (m-80) cc_final: 0.6898 (m-80) REVERT: A 218 LEU cc_start: 0.8318 (tp) cc_final: 0.8001 (tt) REVERT: A 265 THR cc_start: 0.7922 (p) cc_final: 0.7624 (p) REVERT: A 344 SER cc_start: 0.8053 (t) cc_final: 0.7666 (p) REVERT: A 346 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6971 (mt-10) REVERT: A 403 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7005 (m-70) REVERT: A 433 THR cc_start: 0.8201 (m) cc_final: 0.7972 (p) REVERT: A 530 LYS cc_start: 0.7253 (ttmt) cc_final: 0.6767 (ttpp) REVERT: A 532 LYS cc_start: 0.7913 (ttpp) cc_final: 0.7671 (ttpp) REVERT: A 533 LEU cc_start: 0.8486 (tp) cc_final: 0.8236 (tp) REVERT: A 543 HIS cc_start: 0.6834 (m170) cc_final: 0.6625 (m170) REVERT: A 570 LYS cc_start: 0.7768 (ptpt) cc_final: 0.7518 (ptpt) REVERT: A 574 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6446 (mm-30) REVERT: A 575 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7722 (mtpt) REVERT: B 80 ARG cc_start: 0.7183 (mtt-85) cc_final: 0.6482 (mtt-85) REVERT: B 101 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7925 (pt) REVERT: B 117 TRP cc_start: 0.7009 (m100) cc_final: 0.5825 (m100) REVERT: B 125 ASP cc_start: 0.7929 (m-30) cc_final: 0.7527 (m-30) REVERT: B 142 GLU cc_start: 0.7628 (pt0) cc_final: 0.6927 (pt0) REVERT: B 145 ILE cc_start: 0.8183 (mt) cc_final: 0.7765 (mm) REVERT: B 150 LEU cc_start: 0.8318 (tp) cc_final: 0.8038 (tp) REVERT: B 174 MET cc_start: 0.6792 (mtp) cc_final: 0.6409 (mtp) REVERT: B 183 MET cc_start: 0.6756 (mmm) cc_final: 0.6394 (mmm) REVERT: B 190 MET cc_start: 0.7808 (tpp) cc_final: 0.7399 (tpp) REVERT: B 198 TYR cc_start: 0.6894 (m-80) cc_final: 0.6555 (m-80) REVERT: B 237 ASP cc_start: 0.7254 (m-30) cc_final: 0.6888 (m-30) REVERT: B 265 THR cc_start: 0.7578 (t) cc_final: 0.7243 (t) REVERT: B 266 PHE cc_start: 0.7170 (t80) cc_final: 0.6815 (t80) REVERT: B 306 ILE cc_start: 0.7789 (mp) cc_final: 0.7572 (pt) REVERT: B 382 ARG cc_start: 0.7540 (mmt90) cc_final: 0.7036 (mmp80) REVERT: B 383 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7341 (tm-30) REVERT: B 469 ILE cc_start: 0.8004 (mt) cc_final: 0.7694 (mp) REVERT: B 470 TRP cc_start: 0.8217 (p90) cc_final: 0.7980 (p90) REVERT: B 501 LYS cc_start: 0.7778 (tttt) cc_final: 0.7320 (tttt) REVERT: B 509 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6295 (mm-30) REVERT: B 527 PHE cc_start: 0.6988 (p90) cc_final: 0.6440 (p90) REVERT: B 530 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8135 (ttmt) REVERT: B 532 LYS cc_start: 0.7538 (tttm) cc_final: 0.7243 (tttm) REVERT: B 533 LEU cc_start: 0.7749 (tp) cc_final: 0.7381 (tp) REVERT: B 536 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7781 (ttpp) REVERT: B 549 GLN cc_start: 0.7652 (mp10) cc_final: 0.7062 (mp10) REVERT: B 551 MET cc_start: 0.5954 (mmt) cc_final: 0.5391 (mmt) REVERT: E 45 PHE cc_start: 0.7370 (t80) cc_final: 0.6713 (t80) REVERT: E 46 ASN cc_start: 0.7554 (t0) cc_final: 0.7267 (t0) REVERT: E 87 MET cc_start: 0.7304 (ttt) cc_final: 0.6825 (ttt) REVERT: E 166 ASN cc_start: 0.6972 (m110) cc_final: 0.6745 (m110) REVERT: E 190 MET cc_start: 0.5531 (mtm) cc_final: 0.5150 (mtm) REVERT: E 378 TYR cc_start: 0.7039 (m-80) cc_final: 0.6359 (m-80) REVERT: E 398 PHE cc_start: 0.7819 (p90) cc_final: 0.7439 (p90) REVERT: E 527 PHE cc_start: 0.7322 (p90) cc_final: 0.7050 (p90) REVERT: E 528 TRP cc_start: 0.6776 (m100) cc_final: 0.6493 (m100) REVERT: E 561 TYR cc_start: 0.8322 (m-80) cc_final: 0.7734 (m-80) REVERT: I 47 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7013 (t0) REVERT: I 52 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7464 (ttmm) REVERT: I 53 PHE cc_start: 0.7958 (m-80) cc_final: 0.7624 (m-80) REVERT: I 60 GLU cc_start: 0.7388 (tt0) cc_final: 0.7063 (tt0) REVERT: I 87 MET cc_start: 0.6542 (ttp) cc_final: 0.6106 (ttp) REVERT: I 115 ASN cc_start: 0.7586 (t0) cc_final: 0.7252 (t0) REVERT: I 144 GLU cc_start: 0.7315 (pt0) cc_final: 0.7020 (pt0) REVERT: I 174 MET cc_start: 0.7070 (mtp) cc_final: 0.6631 (mtp) REVERT: I 193 GLU cc_start: 0.7256 (mt-10) cc_final: 0.7055 (mt-10) REVERT: I 268 PHE cc_start: 0.7725 (m-80) cc_final: 0.7298 (m-80) REVERT: I 273 CYS cc_start: 0.7509 (t) cc_final: 0.7301 (t) REVERT: I 331 MET cc_start: 0.7274 (ttm) cc_final: 0.7050 (ttm) REVERT: I 386 GLN cc_start: 0.8175 (tt0) cc_final: 0.7931 (tt0) REVERT: I 387 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8154 (ttmm) REVERT: I 396 GLU cc_start: 0.7544 (tt0) cc_final: 0.7058 (tt0) REVERT: I 444 TYR cc_start: 0.7593 (p90) cc_final: 0.7128 (p90) REVERT: I 468 GLN cc_start: 0.7172 (mm110) cc_final: 0.6948 (mm110) REVERT: I 538 LYS cc_start: 0.8075 (tttp) cc_final: 0.7781 (ttmm) REVERT: I 539 LEU cc_start: 0.8600 (mt) cc_final: 0.8237 (mp) REVERT: I 544 THR cc_start: 0.7876 (p) cc_final: 0.7413 (p) REVERT: I 546 ASN cc_start: 0.7964 (p0) cc_final: 0.7729 (p0) REVERT: I 573 TYR cc_start: 0.8285 (p90) cc_final: 0.7805 (p90) REVERT: I 575 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7736 (mtmm) REVERT: I 576 SER cc_start: 0.7895 (t) cc_final: 0.7616 (p) REVERT: F 52 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7396 (ttmm) REVERT: F 59 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.7966 (p) REVERT: F 60 GLU cc_start: 0.7628 (tt0) cc_final: 0.7189 (tt0) REVERT: F 96 MET cc_start: 0.7621 (mpp) cc_final: 0.7111 (mpp) REVERT: F 101 ILE cc_start: 0.8384 (mm) cc_final: 0.8019 (mm) REVERT: F 143 GLN cc_start: 0.7272 (mp10) cc_final: 0.6927 (mp10) REVERT: F 180 ASN cc_start: 0.7696 (t0) cc_final: 0.7309 (t0) REVERT: F 213 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7339 (tm-30) REVERT: F 245 THR cc_start: 0.7622 (t) cc_final: 0.7419 (p) REVERT: F 248 ASN cc_start: 0.7222 (m-40) cc_final: 0.6800 (t0) REVERT: F 266 PHE cc_start: 0.7770 (t80) cc_final: 0.7459 (t80) REVERT: F 271 LYS cc_start: 0.8284 (mtpp) cc_final: 0.8023 (mtpp) REVERT: F 311 ASP cc_start: 0.7021 (p0) cc_final: 0.6566 (p0) REVERT: F 312 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8097 (ptpp) REVERT: F 327 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6669 (mm-30) REVERT: F 335 GLU cc_start: 0.7137 (tt0) cc_final: 0.6867 (tt0) REVERT: F 425 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8191 (p) REVERT: F 459 ASN cc_start: 0.8269 (t0) cc_final: 0.8034 (t0) REVERT: F 475 ASP cc_start: 0.7202 (t0) cc_final: 0.6663 (t0) REVERT: F 484 VAL cc_start: 0.8487 (m) cc_final: 0.8077 (p) REVERT: F 491 GLN cc_start: 0.7882 (mm110) cc_final: 0.7550 (mm110) REVERT: F 551 MET cc_start: 0.6334 (ttt) cc_final: 0.5820 (ttt) REVERT: F 569 MET cc_start: 0.5731 (mmm) cc_final: 0.5465 (mmm) REVERT: C 174 MET cc_start: 0.7293 (mtp) cc_final: 0.6728 (mtp) outliers start: 106 outliers final: 75 residues processed: 796 average time/residue: 0.4097 time to fit residues: 507.8803 Evaluate side-chains 844 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 761 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain G residue 570 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 553 ILE Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 314 optimal weight: 40.0000 chunk 261 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN E 85 ASN ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 HIS ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN F 318 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.152 26519 Z= 0.522 Angle : 0.669 11.373 36251 Z= 0.344 Chirality : 0.047 0.197 3973 Planarity : 0.005 0.056 4735 Dihedral : 5.957 68.997 3509 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.51 % Allowed : 15.38 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 2990 helix: -0.30 (0.50), residues: 100 sheet: -0.49 (0.18), residues: 772 loop : -0.54 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 545 HIS 0.009 0.001 HIS I 384 PHE 0.028 0.002 PHE A 353 TYR 0.037 0.002 TYR G 524 ARG 0.014 0.001 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 759 time to evaluate : 2.798 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: G 59 VAL cc_start: 0.8787 (t) cc_final: 0.8432 (m) REVERT: G 60 GLU cc_start: 0.7145 (tt0) cc_final: 0.6910 (tt0) REVERT: G 125 ASP cc_start: 0.6776 (m-30) cc_final: 0.6432 (m-30) REVERT: G 135 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6945 (mt-10) REVERT: G 142 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6606 (mm-30) REVERT: G 174 MET cc_start: 0.7442 (mtp) cc_final: 0.7177 (mtp) REVERT: G 217 THR cc_start: 0.7830 (p) cc_final: 0.7501 (p) REVERT: G 239 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: G 248 ASN cc_start: 0.7744 (t0) cc_final: 0.7504 (t0) REVERT: G 271 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7742 (mtpp) REVERT: G 319 MET cc_start: 0.2673 (OUTLIER) cc_final: 0.2320 (ptm) REVERT: G 382 ARG cc_start: 0.5715 (mtm180) cc_final: 0.5223 (mtm180) REVERT: G 409 TYR cc_start: 0.7999 (t80) cc_final: 0.7595 (t80) REVERT: G 473 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6596 (tm-30) REVERT: G 536 LYS cc_start: 0.8319 (ttpp) cc_final: 0.7873 (ttpp) REVERT: G 559 PHE cc_start: 0.8107 (m-80) cc_final: 0.7431 (m-80) REVERT: G 560 ASN cc_start: 0.7837 (m-40) cc_final: 0.7410 (m-40) REVERT: G 581 ARG cc_start: 0.8307 (ttp-110) cc_final: 0.7909 (ttp-110) REVERT: A 56 ASN cc_start: 0.7622 (m110) cc_final: 0.7370 (m110) REVERT: A 66 SER cc_start: 0.7609 (OUTLIER) cc_final: 0.7032 (m) REVERT: A 98 LEU cc_start: 0.7742 (mt) cc_final: 0.7104 (mt) REVERT: A 99 ASP cc_start: 0.7079 (t70) cc_final: 0.6838 (t70) REVERT: A 100 ASP cc_start: 0.6854 (m-30) cc_final: 0.6296 (m-30) REVERT: A 127 GLN cc_start: 0.7673 (tt0) cc_final: 0.7449 (tt0) REVERT: A 174 MET cc_start: 0.7390 (mtp) cc_final: 0.6918 (mtp) REVERT: A 183 MET cc_start: 0.7160 (mmm) cc_final: 0.6618 (mmm) REVERT: A 211 TYR cc_start: 0.7383 (m-80) cc_final: 0.7021 (m-80) REVERT: A 218 LEU cc_start: 0.8290 (tp) cc_final: 0.7833 (tt) REVERT: A 306 ILE cc_start: 0.8778 (tp) cc_final: 0.8514 (tt) REVERT: A 344 SER cc_start: 0.7973 (t) cc_final: 0.7414 (p) REVERT: A 433 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 443 ASN cc_start: 0.7460 (p0) cc_final: 0.7226 (p0) REVERT: A 448 PHE cc_start: 0.8006 (t80) cc_final: 0.7781 (t80) REVERT: A 471 ASP cc_start: 0.6725 (t0) cc_final: 0.6185 (t0) REVERT: A 473 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7336 (tm-30) REVERT: A 475 ASP cc_start: 0.7563 (t70) cc_final: 0.6809 (t0) REVERT: A 530 LYS cc_start: 0.7462 (ttmt) cc_final: 0.6954 (ttpp) REVERT: A 533 LEU cc_start: 0.8531 (tp) cc_final: 0.8294 (tp) REVERT: A 569 MET cc_start: 0.5653 (mmm) cc_final: 0.5346 (mmm) REVERT: A 574 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6327 (mm-30) REVERT: B 80 ARG cc_start: 0.7196 (mtt-85) cc_final: 0.6494 (mtt-85) REVERT: B 101 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7929 (pt) REVERT: B 117 TRP cc_start: 0.7128 (m100) cc_final: 0.6001 (m100) REVERT: B 142 GLU cc_start: 0.7747 (pt0) cc_final: 0.7081 (pt0) REVERT: B 145 ILE cc_start: 0.8133 (mt) cc_final: 0.7853 (mm) REVERT: B 150 LEU cc_start: 0.8331 (tp) cc_final: 0.8094 (tp) REVERT: B 151 LYS cc_start: 0.7853 (mttm) cc_final: 0.7570 (tttm) REVERT: B 174 MET cc_start: 0.6806 (mtp) cc_final: 0.6414 (mtp) REVERT: B 183 MET cc_start: 0.6834 (mmm) cc_final: 0.6349 (mmm) REVERT: B 190 MET cc_start: 0.7766 (tpp) cc_final: 0.7376 (tpp) REVERT: B 198 TYR cc_start: 0.6829 (m-80) cc_final: 0.6585 (m-80) REVERT: B 265 THR cc_start: 0.7630 (t) cc_final: 0.7273 (t) REVERT: B 266 PHE cc_start: 0.7281 (t80) cc_final: 0.6763 (t80) REVERT: B 306 ILE cc_start: 0.7805 (mp) cc_final: 0.7591 (pt) REVERT: B 342 TYR cc_start: 0.7216 (p90) cc_final: 0.6989 (p90) REVERT: B 469 ILE cc_start: 0.8077 (mt) cc_final: 0.7867 (mp) REVERT: B 470 TRP cc_start: 0.8257 (p90) cc_final: 0.7947 (p90) REVERT: B 501 LYS cc_start: 0.7842 (tttt) cc_final: 0.7410 (tttt) REVERT: B 527 PHE cc_start: 0.6961 (p90) cc_final: 0.6465 (p90) REVERT: B 530 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8163 (ttmt) REVERT: B 532 LYS cc_start: 0.7633 (tttm) cc_final: 0.7256 (tttm) REVERT: B 533 LEU cc_start: 0.7745 (tp) cc_final: 0.7346 (tp) REVERT: B 536 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7811 (ttpp) REVERT: B 551 MET cc_start: 0.5919 (mmt) cc_final: 0.5443 (mmt) REVERT: E 45 PHE cc_start: 0.7432 (t80) cc_final: 0.6862 (t80) REVERT: E 46 ASN cc_start: 0.7515 (t0) cc_final: 0.7232 (t0) REVERT: E 121 PHE cc_start: 0.7733 (m-80) cc_final: 0.7159 (m-10) REVERT: E 190 MET cc_start: 0.5676 (mtm) cc_final: 0.5247 (mtm) REVERT: E 378 TYR cc_start: 0.7124 (m-80) cc_final: 0.6400 (m-80) REVERT: E 398 PHE cc_start: 0.7860 (p90) cc_final: 0.7431 (p90) REVERT: E 527 PHE cc_start: 0.7397 (p90) cc_final: 0.7117 (p90) REVERT: E 528 TRP cc_start: 0.6816 (m100) cc_final: 0.6524 (m100) REVERT: E 561 TYR cc_start: 0.8332 (m-80) cc_final: 0.7646 (m-80) REVERT: I 47 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7375 (t0) REVERT: I 52 LYS cc_start: 0.7704 (ttmm) cc_final: 0.7425 (ttmm) REVERT: I 53 PHE cc_start: 0.7936 (m-80) cc_final: 0.7626 (m-80) REVERT: I 60 GLU cc_start: 0.7407 (tt0) cc_final: 0.7105 (tt0) REVERT: I 87 MET cc_start: 0.6708 (ttp) cc_final: 0.6262 (ttp) REVERT: I 115 ASN cc_start: 0.7595 (t0) cc_final: 0.6960 (t0) REVERT: I 144 GLU cc_start: 0.7369 (pt0) cc_final: 0.7067 (pt0) REVERT: I 174 MET cc_start: 0.7072 (mtp) cc_final: 0.6674 (mtp) REVERT: I 193 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7065 (mt-10) REVERT: I 268 PHE cc_start: 0.7738 (m-80) cc_final: 0.7349 (m-80) REVERT: I 273 CYS cc_start: 0.7548 (t) cc_final: 0.7345 (t) REVERT: I 319 MET cc_start: 0.5367 (tpp) cc_final: 0.4628 (tpp) REVERT: I 331 MET cc_start: 0.7239 (ttm) cc_final: 0.7030 (ttm) REVERT: I 383 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: I 387 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8164 (ttmm) REVERT: I 396 GLU cc_start: 0.7567 (tt0) cc_final: 0.7107 (tt0) REVERT: I 444 TYR cc_start: 0.7819 (p90) cc_final: 0.7388 (p90) REVERT: I 538 LYS cc_start: 0.8105 (tttp) cc_final: 0.7841 (ttmm) REVERT: I 544 THR cc_start: 0.7917 (p) cc_final: 0.7486 (p) REVERT: I 549 GLN cc_start: 0.8141 (tt0) cc_final: 0.7662 (tt0) REVERT: I 550 GLN cc_start: 0.7683 (mt0) cc_final: 0.7371 (mm110) REVERT: I 573 TYR cc_start: 0.8267 (p90) cc_final: 0.7764 (p90) REVERT: I 575 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7769 (mtmm) REVERT: F 52 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7498 (ttmm) REVERT: F 60 GLU cc_start: 0.7643 (tt0) cc_final: 0.7259 (tt0) REVERT: F 96 MET cc_start: 0.7668 (mpp) cc_final: 0.7059 (mpp) REVERT: F 143 GLN cc_start: 0.7430 (mp10) cc_final: 0.7150 (mp10) REVERT: F 180 ASN cc_start: 0.7737 (t0) cc_final: 0.7368 (t0) REVERT: F 213 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7326 (tm-30) REVERT: F 248 ASN cc_start: 0.7267 (m-40) cc_final: 0.6790 (t0) REVERT: F 266 PHE cc_start: 0.7828 (t80) cc_final: 0.7433 (t80) REVERT: F 271 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7965 (mtpp) REVERT: F 275 LEU cc_start: 0.7619 (mp) cc_final: 0.7396 (mt) REVERT: F 276 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7274 (m) REVERT: F 280 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7731 (mm-40) REVERT: F 327 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6786 (mm-30) REVERT: F 335 GLU cc_start: 0.7226 (tt0) cc_final: 0.6955 (tt0) REVERT: F 425 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8246 (p) REVERT: F 475 ASP cc_start: 0.7207 (t0) cc_final: 0.6650 (t0) REVERT: F 484 VAL cc_start: 0.8585 (m) cc_final: 0.8189 (p) REVERT: F 551 MET cc_start: 0.6410 (ttt) cc_final: 0.5871 (ttt) REVERT: F 569 MET cc_start: 0.5736 (mmm) cc_final: 0.5458 (mmm) REVERT: C 174 MET cc_start: 0.7348 (mtp) cc_final: 0.6787 (mtp) REVERT: C 213 GLN cc_start: 0.7091 (tm-30) cc_final: 0.6742 (tm-30) outliers start: 123 outliers final: 90 residues processed: 791 average time/residue: 0.3804 time to fit residues: 465.3141 Evaluate side-chains 853 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 753 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 466 ASN Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 524 TYR Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain G residue 570 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 383 GLN Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 553 ILE Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 577 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 179 optimal weight: 50.0000 chunk 229 optimal weight: 0.2980 chunk 177 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 313 optimal weight: 30.0000 chunk 196 optimal weight: 20.0000 chunk 190 optimal weight: 50.0000 chunk 144 optimal weight: 0.3980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26519 Z= 0.214 Angle : 0.563 8.337 36251 Z= 0.284 Chirality : 0.042 0.165 3973 Planarity : 0.005 0.049 4735 Dihedral : 5.423 69.118 3509 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.81 % Allowed : 17.11 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2990 helix: -0.16 (0.50), residues: 100 sheet: -0.42 (0.19), residues: 768 loop : -0.33 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP F 545 HIS 0.005 0.001 HIS F 277 PHE 0.031 0.002 PHE G 45 TYR 0.030 0.002 TYR F 233 ARG 0.011 0.000 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 759 time to evaluate : 2.526 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: G 59 VAL cc_start: 0.8790 (t) cc_final: 0.8429 (m) REVERT: G 60 GLU cc_start: 0.7058 (tt0) cc_final: 0.6822 (tt0) REVERT: G 90 THR cc_start: 0.8571 (t) cc_final: 0.8325 (t) REVERT: G 125 ASP cc_start: 0.6650 (m-30) cc_final: 0.6336 (m-30) REVERT: G 135 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6916 (mt-10) REVERT: G 142 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6670 (mm-30) REVERT: G 185 PHE cc_start: 0.8188 (t80) cc_final: 0.7867 (t80) REVERT: G 211 TYR cc_start: 0.8199 (m-80) cc_final: 0.7818 (m-80) REVERT: G 217 THR cc_start: 0.7772 (p) cc_final: 0.7431 (p) REVERT: G 239 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6657 (m-30) REVERT: G 248 ASN cc_start: 0.7660 (t0) cc_final: 0.7401 (t0) REVERT: G 271 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7775 (mtpp) REVERT: G 319 MET cc_start: 0.2549 (OUTLIER) cc_final: 0.2224 (ptm) REVERT: G 382 ARG cc_start: 0.5642 (mtm180) cc_final: 0.5116 (mtm180) REVERT: G 390 THR cc_start: 0.8666 (t) cc_final: 0.8401 (p) REVERT: G 409 TYR cc_start: 0.8023 (t80) cc_final: 0.7746 (t80) REVERT: G 413 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6378 (p0) REVERT: G 473 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6554 (tm-30) REVERT: G 536 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7754 (ttpp) REVERT: G 560 ASN cc_start: 0.7853 (m-40) cc_final: 0.7447 (m-40) REVERT: G 581 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7903 (ttp-110) REVERT: A 56 ASN cc_start: 0.7436 (m110) cc_final: 0.7184 (m110) REVERT: A 66 SER cc_start: 0.7533 (m) cc_final: 0.7011 (m) REVERT: A 100 ASP cc_start: 0.6721 (m-30) cc_final: 0.6192 (m-30) REVERT: A 168 ASP cc_start: 0.5532 (OUTLIER) cc_final: 0.5081 (m-30) REVERT: A 174 MET cc_start: 0.7424 (mtp) cc_final: 0.6718 (mtp) REVERT: A 183 MET cc_start: 0.7097 (mmm) cc_final: 0.6534 (mmm) REVERT: A 211 TYR cc_start: 0.7253 (m-80) cc_final: 0.6931 (m-80) REVERT: A 218 LEU cc_start: 0.8289 (tp) cc_final: 0.7968 (tt) REVERT: A 346 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6926 (mp0) REVERT: A 403 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7079 (m-70) REVERT: A 433 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7955 (p) REVERT: A 475 ASP cc_start: 0.7425 (t70) cc_final: 0.6627 (t0) REVERT: A 530 LYS cc_start: 0.7296 (ttmt) cc_final: 0.6832 (ttpp) REVERT: A 533 LEU cc_start: 0.8491 (tp) cc_final: 0.8253 (tp) REVERT: A 569 MET cc_start: 0.5549 (mmm) cc_final: 0.5264 (mmm) REVERT: A 574 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6231 (mm-30) REVERT: A 575 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7726 (mtpt) REVERT: B 80 ARG cc_start: 0.7169 (mtt-85) cc_final: 0.6478 (mtt-85) REVERT: B 101 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7926 (pt) REVERT: B 117 TRP cc_start: 0.7073 (m100) cc_final: 0.6230 (m100) REVERT: B 125 ASP cc_start: 0.7917 (m-30) cc_final: 0.7500 (m-30) REVERT: B 142 GLU cc_start: 0.7724 (pt0) cc_final: 0.7125 (pt0) REVERT: B 145 ILE cc_start: 0.8142 (mt) cc_final: 0.7869 (mm) REVERT: B 150 LEU cc_start: 0.8309 (tp) cc_final: 0.8041 (tp) REVERT: B 151 LYS cc_start: 0.7823 (mttm) cc_final: 0.7529 (tttm) REVERT: B 174 MET cc_start: 0.6745 (mtp) cc_final: 0.6317 (mtp) REVERT: B 183 MET cc_start: 0.6805 (mmm) cc_final: 0.6332 (mmm) REVERT: B 190 MET cc_start: 0.7753 (tpp) cc_final: 0.7354 (tpp) REVERT: B 247 GLU cc_start: 0.6159 (mp0) cc_final: 0.5566 (mp0) REVERT: B 265 THR cc_start: 0.7696 (t) cc_final: 0.7332 (t) REVERT: B 266 PHE cc_start: 0.7290 (t80) cc_final: 0.6793 (t80) REVERT: B 306 ILE cc_start: 0.7766 (mp) cc_final: 0.7552 (pt) REVERT: B 342 TYR cc_start: 0.7216 (p90) cc_final: 0.6888 (p90) REVERT: B 382 ARG cc_start: 0.7855 (mmp80) cc_final: 0.7390 (mmp80) REVERT: B 470 TRP cc_start: 0.8228 (p90) cc_final: 0.7938 (p90) REVERT: B 501 LYS cc_start: 0.7896 (tttt) cc_final: 0.7428 (tttt) REVERT: B 527 PHE cc_start: 0.6897 (p90) cc_final: 0.6397 (p90) REVERT: B 530 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8162 (ttmt) REVERT: B 532 LYS cc_start: 0.7606 (tttm) cc_final: 0.7227 (tttm) REVERT: B 533 LEU cc_start: 0.7733 (tp) cc_final: 0.7320 (tp) REVERT: B 536 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7793 (ttpp) REVERT: B 551 MET cc_start: 0.5789 (mmt) cc_final: 0.5303 (mmt) REVERT: E 45 PHE cc_start: 0.7369 (t80) cc_final: 0.6732 (t80) REVERT: E 46 ASN cc_start: 0.7547 (t0) cc_final: 0.7280 (t0) REVERT: E 121 PHE cc_start: 0.7786 (m-80) cc_final: 0.7206 (m-10) REVERT: E 190 MET cc_start: 0.5659 (mtm) cc_final: 0.5230 (mtm) REVERT: E 378 TYR cc_start: 0.7080 (m-80) cc_final: 0.6391 (m-80) REVERT: E 398 PHE cc_start: 0.7781 (p90) cc_final: 0.7406 (p90) REVERT: E 527 PHE cc_start: 0.7350 (p90) cc_final: 0.7139 (p90) REVERT: E 528 TRP cc_start: 0.6760 (m100) cc_final: 0.6457 (m100) REVERT: E 559 PHE cc_start: 0.7125 (m-80) cc_final: 0.6842 (m-80) REVERT: E 561 TYR cc_start: 0.8354 (m-80) cc_final: 0.7707 (m-80) REVERT: I 47 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7267 (t0) REVERT: I 52 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7429 (ttmm) REVERT: I 53 PHE cc_start: 0.7903 (m-80) cc_final: 0.7575 (m-80) REVERT: I 60 GLU cc_start: 0.7421 (tt0) cc_final: 0.7101 (tt0) REVERT: I 87 MET cc_start: 0.6695 (ttp) cc_final: 0.6260 (ttp) REVERT: I 115 ASN cc_start: 0.7487 (t0) cc_final: 0.7111 (t0) REVERT: I 142 GLU cc_start: 0.7551 (pt0) cc_final: 0.7300 (pt0) REVERT: I 144 GLU cc_start: 0.7300 (pt0) cc_final: 0.6993 (pt0) REVERT: I 174 MET cc_start: 0.7036 (mtp) cc_final: 0.6645 (mtp) REVERT: I 198 TYR cc_start: 0.7744 (m-80) cc_final: 0.7301 (m-80) REVERT: I 268 PHE cc_start: 0.7664 (m-80) cc_final: 0.7301 (m-80) REVERT: I 319 MET cc_start: 0.5169 (tpp) cc_final: 0.4495 (tpp) REVERT: I 331 MET cc_start: 0.7249 (ttm) cc_final: 0.7020 (ttm) REVERT: I 383 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7383 (mt0) REVERT: I 387 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8175 (ttmm) REVERT: I 396 GLU cc_start: 0.7518 (tt0) cc_final: 0.7001 (tt0) REVERT: I 444 TYR cc_start: 0.7869 (p90) cc_final: 0.7438 (p90) REVERT: I 468 GLN cc_start: 0.7215 (mm110) cc_final: 0.6995 (mm110) REVERT: I 538 LYS cc_start: 0.8088 (tttp) cc_final: 0.7833 (ttmm) REVERT: I 544 THR cc_start: 0.7938 (p) cc_final: 0.7677 (p) REVERT: I 546 ASN cc_start: 0.8115 (p0) cc_final: 0.7828 (p0) REVERT: I 549 GLN cc_start: 0.7945 (tt0) cc_final: 0.7568 (tt0) REVERT: I 573 TYR cc_start: 0.8301 (p90) cc_final: 0.7806 (p90) REVERT: I 575 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7777 (mtmm) REVERT: F 52 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7394 (ttmm) REVERT: F 60 GLU cc_start: 0.7495 (tt0) cc_final: 0.7136 (tt0) REVERT: F 96 MET cc_start: 0.7607 (mpp) cc_final: 0.7159 (mpp) REVERT: F 143 GLN cc_start: 0.7387 (mp10) cc_final: 0.7027 (mp10) REVERT: F 180 ASN cc_start: 0.7697 (t0) cc_final: 0.7314 (t0) REVERT: F 213 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7366 (tm-30) REVERT: F 242 GLN cc_start: 0.7384 (mt0) cc_final: 0.7050 (mt0) REVERT: F 248 ASN cc_start: 0.7193 (m-40) cc_final: 0.6818 (t0) REVERT: F 266 PHE cc_start: 0.7671 (t80) cc_final: 0.7384 (t80) REVERT: F 271 LYS cc_start: 0.8263 (mtpp) cc_final: 0.8015 (mtpp) REVERT: F 276 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7192 (m) REVERT: F 280 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7537 (mm110) REVERT: F 327 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6736 (mm-30) REVERT: F 475 ASP cc_start: 0.7137 (t0) cc_final: 0.6607 (t0) REVERT: F 484 VAL cc_start: 0.8495 (m) cc_final: 0.8109 (p) REVERT: F 491 GLN cc_start: 0.7832 (mm110) cc_final: 0.7530 (mm110) REVERT: F 551 MET cc_start: 0.6318 (ttt) cc_final: 0.5785 (ttt) REVERT: F 569 MET cc_start: 0.5709 (mmm) cc_final: 0.5444 (mmm) REVERT: C 174 MET cc_start: 0.7288 (mtp) cc_final: 0.6787 (mtp) REVERT: C 250 VAL cc_start: 0.7367 (t) cc_final: 0.7133 (t) outliers start: 104 outliers final: 75 residues processed: 788 average time/residue: 0.3937 time to fit residues: 479.7302 Evaluate side-chains 841 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 755 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 383 GLN Chi-restraints excluded: chain I residue 553 ILE Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 7.9990 chunk 125 optimal weight: 50.0000 chunk 187 optimal weight: 0.0370 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 199 optimal weight: 40.0000 chunk 213 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 246 optimal weight: 20.0000 overall best weight: 3.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 ASN A 47 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS A 546 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 26519 Z= 0.413 Angle : 0.627 8.848 36251 Z= 0.321 Chirality : 0.045 0.191 3973 Planarity : 0.005 0.059 4735 Dihedral : 5.687 69.786 3509 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.10 % Allowed : 17.40 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.67 (0.15), residues: 2990 helix: -0.24 (0.50), residues: 100 sheet: -0.46 (0.19), residues: 775 loop : -0.42 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 545 HIS 0.007 0.001 HIS F 277 PHE 0.031 0.002 PHE A 353 TYR 0.037 0.002 TYR A 342 ARG 0.013 0.001 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 766 time to evaluate : 2.617 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: G 59 VAL cc_start: 0.8782 (t) cc_final: 0.8431 (m) REVERT: G 60 GLU cc_start: 0.7174 (tt0) cc_final: 0.6932 (tt0) REVERT: G 125 ASP cc_start: 0.6723 (m-30) cc_final: 0.6381 (m-30) REVERT: G 142 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6773 (mm-30) REVERT: G 217 THR cc_start: 0.7804 (p) cc_final: 0.7465 (p) REVERT: G 239 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: G 248 ASN cc_start: 0.7655 (t0) cc_final: 0.7412 (t0) REVERT: G 271 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7768 (mtpp) REVERT: G 319 MET cc_start: 0.2714 (OUTLIER) cc_final: 0.2327 (ptm) REVERT: G 382 ARG cc_start: 0.5743 (mtm180) cc_final: 0.5234 (mtm180) REVERT: G 390 THR cc_start: 0.8657 (t) cc_final: 0.8352 (p) REVERT: G 409 TYR cc_start: 0.8056 (t80) cc_final: 0.7715 (t80) REVERT: G 413 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6360 (p0) REVERT: G 473 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6584 (tm-30) REVERT: G 536 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7894 (ttpp) REVERT: G 559 PHE cc_start: 0.8109 (m-80) cc_final: 0.7761 (m-80) REVERT: G 560 ASN cc_start: 0.7841 (m-40) cc_final: 0.7418 (m-40) REVERT: A 56 ASN cc_start: 0.7591 (m110) cc_final: 0.7348 (m110) REVERT: A 66 SER cc_start: 0.7534 (m) cc_final: 0.7012 (m) REVERT: A 98 LEU cc_start: 0.7746 (mt) cc_final: 0.7156 (mt) REVERT: A 99 ASP cc_start: 0.7141 (t70) cc_final: 0.6928 (t70) REVERT: A 100 ASP cc_start: 0.6611 (m-30) cc_final: 0.6053 (m-30) REVERT: A 168 ASP cc_start: 0.5593 (OUTLIER) cc_final: 0.5147 (m-30) REVERT: A 174 MET cc_start: 0.7389 (mtp) cc_final: 0.6717 (mtp) REVERT: A 183 MET cc_start: 0.7199 (mmm) cc_final: 0.6665 (mmm) REVERT: A 211 TYR cc_start: 0.7356 (m-80) cc_final: 0.7021 (m-80) REVERT: A 218 LEU cc_start: 0.8304 (tp) cc_final: 0.7869 (tt) REVERT: A 306 ILE cc_start: 0.8787 (tp) cc_final: 0.8479 (tt) REVERT: A 313 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7867 (mtt-85) REVERT: A 346 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6955 (mp0) REVERT: A 433 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8014 (p) REVERT: A 473 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7264 (tm-30) REVERT: A 475 ASP cc_start: 0.7548 (t70) cc_final: 0.6815 (t0) REVERT: A 530 LYS cc_start: 0.7312 (ttmt) cc_final: 0.6887 (ttpp) REVERT: A 533 LEU cc_start: 0.8518 (tp) cc_final: 0.8279 (tp) REVERT: A 569 MET cc_start: 0.5619 (mmm) cc_final: 0.5332 (mmm) REVERT: A 574 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6347 (mm-30) REVERT: A 575 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7974 (mtpt) REVERT: B 80 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6453 (mtt-85) REVERT: B 101 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7922 (pt) REVERT: B 117 TRP cc_start: 0.6906 (m100) cc_final: 0.6366 (m100) REVERT: B 125 ASP cc_start: 0.7957 (m-30) cc_final: 0.7539 (m-30) REVERT: B 142 GLU cc_start: 0.7746 (pt0) cc_final: 0.7225 (pt0) REVERT: B 145 ILE cc_start: 0.8119 (mt) cc_final: 0.7856 (mm) REVERT: B 150 LEU cc_start: 0.8323 (tp) cc_final: 0.8086 (tp) REVERT: B 151 LYS cc_start: 0.7877 (mttm) cc_final: 0.7566 (tttm) REVERT: B 174 MET cc_start: 0.6746 (mtp) cc_final: 0.6367 (mtp) REVERT: B 183 MET cc_start: 0.6805 (mmm) cc_final: 0.6356 (mmm) REVERT: B 190 MET cc_start: 0.7742 (tpp) cc_final: 0.7344 (tpp) REVERT: B 247 GLU cc_start: 0.6178 (mp0) cc_final: 0.5601 (mp0) REVERT: B 266 PHE cc_start: 0.7315 (t80) cc_final: 0.6766 (t80) REVERT: B 470 TRP cc_start: 0.8177 (p90) cc_final: 0.7951 (p90) REVERT: B 501 LYS cc_start: 0.7891 (tttt) cc_final: 0.7452 (tttt) REVERT: B 527 PHE cc_start: 0.6912 (p90) cc_final: 0.6422 (p90) REVERT: B 530 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8194 (ttmt) REVERT: B 532 LYS cc_start: 0.7601 (tttm) cc_final: 0.7227 (tttm) REVERT: B 533 LEU cc_start: 0.7692 (tp) cc_final: 0.7342 (tp) REVERT: B 536 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7786 (ttpp) REVERT: B 551 MET cc_start: 0.5865 (mmt) cc_final: 0.5434 (mmt) REVERT: E 45 PHE cc_start: 0.7406 (t80) cc_final: 0.6852 (t80) REVERT: E 121 PHE cc_start: 0.7787 (m-80) cc_final: 0.7185 (m-10) REVERT: E 190 MET cc_start: 0.5687 (mtm) cc_final: 0.5251 (mtm) REVERT: E 378 TYR cc_start: 0.7132 (m-80) cc_final: 0.6418 (m-80) REVERT: E 398 PHE cc_start: 0.7815 (p90) cc_final: 0.7440 (p90) REVERT: E 455 THR cc_start: 0.4217 (p) cc_final: 0.3674 (m) REVERT: E 527 PHE cc_start: 0.7396 (p90) cc_final: 0.7166 (p90) REVERT: E 528 TRP cc_start: 0.6765 (m100) cc_final: 0.6458 (m100) REVERT: E 561 TYR cc_start: 0.8338 (m-80) cc_final: 0.7651 (m-80) REVERT: I 47 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7381 (t0) REVERT: I 52 LYS cc_start: 0.7718 (ttmm) cc_final: 0.7432 (ttmm) REVERT: I 53 PHE cc_start: 0.7912 (m-80) cc_final: 0.7571 (m-80) REVERT: I 60 GLU cc_start: 0.7438 (tt0) cc_final: 0.7151 (tt0) REVERT: I 87 MET cc_start: 0.6765 (ttp) cc_final: 0.6346 (ttp) REVERT: I 115 ASN cc_start: 0.7536 (t0) cc_final: 0.7110 (t0) REVERT: I 142 GLU cc_start: 0.7563 (pt0) cc_final: 0.7330 (pt0) REVERT: I 144 GLU cc_start: 0.7334 (pt0) cc_final: 0.7036 (pt0) REVERT: I 174 MET cc_start: 0.7072 (mtp) cc_final: 0.6665 (mtp) REVERT: I 268 PHE cc_start: 0.7728 (m-80) cc_final: 0.7377 (m-80) REVERT: I 319 MET cc_start: 0.5503 (tpp) cc_final: 0.4974 (tpp) REVERT: I 331 MET cc_start: 0.7236 (ttm) cc_final: 0.6991 (ttm) REVERT: I 383 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: I 387 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8185 (ttmm) REVERT: I 396 GLU cc_start: 0.7563 (tt0) cc_final: 0.7045 (tt0) REVERT: I 444 TYR cc_start: 0.7920 (p90) cc_final: 0.7569 (p90) REVERT: I 468 GLN cc_start: 0.7398 (mm110) cc_final: 0.7074 (mm110) REVERT: I 538 LYS cc_start: 0.8132 (tttp) cc_final: 0.7889 (ttmm) REVERT: I 544 THR cc_start: 0.7897 (p) cc_final: 0.7663 (p) REVERT: I 546 ASN cc_start: 0.7947 (p0) cc_final: 0.7698 (p0) REVERT: I 549 GLN cc_start: 0.8096 (tt0) cc_final: 0.7642 (tt0) REVERT: I 550 GLN cc_start: 0.7520 (mt0) cc_final: 0.7306 (mm110) REVERT: I 573 TYR cc_start: 0.8324 (p90) cc_final: 0.7810 (p90) REVERT: I 575 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7771 (mtmm) REVERT: F 52 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7422 (ttmm) REVERT: F 60 GLU cc_start: 0.7536 (tt0) cc_final: 0.7191 (tt0) REVERT: F 143 GLN cc_start: 0.7562 (mp10) cc_final: 0.6902 (mp10) REVERT: F 180 ASN cc_start: 0.7700 (t0) cc_final: 0.7254 (t0) REVERT: F 248 ASN cc_start: 0.7256 (m-40) cc_final: 0.6778 (t0) REVERT: F 266 PHE cc_start: 0.7706 (t80) cc_final: 0.7408 (t80) REVERT: F 271 LYS cc_start: 0.8295 (mtpp) cc_final: 0.8071 (mtpp) REVERT: F 275 LEU cc_start: 0.7575 (mp) cc_final: 0.7208 (mp) REVERT: F 276 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7331 (m) REVERT: F 280 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7500 (mm110) REVERT: F 327 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6809 (mm-30) REVERT: F 475 ASP cc_start: 0.7193 (t0) cc_final: 0.6507 (t0) REVERT: F 484 VAL cc_start: 0.8516 (m) cc_final: 0.8131 (p) REVERT: F 491 GLN cc_start: 0.7905 (mm110) cc_final: 0.7428 (mm-40) REVERT: F 551 MET cc_start: 0.6432 (ttt) cc_final: 0.5877 (ttt) REVERT: F 569 MET cc_start: 0.5740 (mmm) cc_final: 0.5463 (mmm) REVERT: C 174 MET cc_start: 0.7322 (mtp) cc_final: 0.6798 (mtp) REVERT: C 213 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6666 (tm-30) REVERT: C 250 VAL cc_start: 0.7413 (t) cc_final: 0.7185 (t) outliers start: 112 outliers final: 82 residues processed: 799 average time/residue: 0.3824 time to fit residues: 471.2046 Evaluate side-chains 851 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 758 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 383 GLN Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 553 ILE Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 577 GLN Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 444 TYR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 284 optimal weight: 20.0000 chunk 300 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 175 optimal weight: 40.0000 chunk 127 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 263 optimal weight: 30.0000 chunk 276 optimal weight: 0.5980 chunk 290 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 248 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 26519 Z= 0.428 Angle : 0.637 9.732 36251 Z= 0.327 Chirality : 0.045 0.183 3973 Planarity : 0.005 0.055 4735 Dihedral : 5.759 70.433 3509 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.29 % Allowed : 17.55 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.73 (0.15), residues: 2990 helix: -0.19 (0.50), residues: 100 sheet: -0.46 (0.19), residues: 763 loop : -0.49 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 545 HIS 0.008 0.001 HIS F 277 PHE 0.041 0.002 PHE A 448 TYR 0.035 0.002 TYR F 233 ARG 0.013 0.001 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 761 time to evaluate : 2.588 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: G 59 VAL cc_start: 0.8792 (t) cc_final: 0.8433 (m) REVERT: G 60 GLU cc_start: 0.7173 (tt0) cc_final: 0.6932 (tt0) REVERT: G 125 ASP cc_start: 0.6727 (m-30) cc_final: 0.6390 (m-30) REVERT: G 142 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6734 (mm-30) REVERT: G 185 PHE cc_start: 0.8198 (t80) cc_final: 0.7947 (t80) REVERT: G 217 THR cc_start: 0.7814 (p) cc_final: 0.7495 (p) REVERT: G 239 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: G 248 ASN cc_start: 0.7663 (t0) cc_final: 0.7419 (t0) REVERT: G 271 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7770 (mtpp) REVERT: G 319 MET cc_start: 0.2746 (OUTLIER) cc_final: 0.2335 (ptm) REVERT: G 382 ARG cc_start: 0.5744 (mtm180) cc_final: 0.5215 (mtm180) REVERT: G 409 TYR cc_start: 0.8091 (t80) cc_final: 0.7740 (t80) REVERT: G 473 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6702 (tm-30) REVERT: G 536 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7805 (ttpp) REVERT: G 560 ASN cc_start: 0.7835 (m-40) cc_final: 0.7418 (m-40) REVERT: A 56 ASN cc_start: 0.7561 (m110) cc_final: 0.7318 (m110) REVERT: A 66 SER cc_start: 0.7551 (m) cc_final: 0.7032 (m) REVERT: A 98 LEU cc_start: 0.7721 (mt) cc_final: 0.7142 (mt) REVERT: A 99 ASP cc_start: 0.7194 (t70) cc_final: 0.6926 (t70) REVERT: A 100 ASP cc_start: 0.6770 (m-30) cc_final: 0.6263 (m-30) REVERT: A 142 GLU cc_start: 0.7514 (pt0) cc_final: 0.7052 (pt0) REVERT: A 168 ASP cc_start: 0.5654 (OUTLIER) cc_final: 0.5211 (m-30) REVERT: A 174 MET cc_start: 0.7432 (mtp) cc_final: 0.6736 (mtp) REVERT: A 183 MET cc_start: 0.7197 (mmm) cc_final: 0.6633 (mmm) REVERT: A 211 TYR cc_start: 0.7352 (m-80) cc_final: 0.7007 (m-80) REVERT: A 218 LEU cc_start: 0.8310 (tp) cc_final: 0.7883 (tt) REVERT: A 306 ILE cc_start: 0.8796 (tp) cc_final: 0.8467 (tt) REVERT: A 313 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7878 (mtt-85) REVERT: A 344 SER cc_start: 0.8195 (t) cc_final: 0.7774 (p) REVERT: A 346 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6956 (mp0) REVERT: A 433 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8003 (p) REVERT: A 473 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 475 ASP cc_start: 0.7518 (t70) cc_final: 0.6782 (t0) REVERT: A 530 LYS cc_start: 0.7360 (ttmt) cc_final: 0.6930 (ttpp) REVERT: A 533 LEU cc_start: 0.8534 (tp) cc_final: 0.8266 (tp) REVERT: A 569 MET cc_start: 0.5620 (mmm) cc_final: 0.5348 (mmm) REVERT: A 574 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6405 (mm-30) REVERT: A 575 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7912 (mtpt) REVERT: B 80 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6505 (mtt-85) REVERT: B 101 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7921 (pt) REVERT: B 117 TRP cc_start: 0.7002 (m100) cc_final: 0.6529 (m100) REVERT: B 125 ASP cc_start: 0.7965 (m-30) cc_final: 0.7532 (m-30) REVERT: B 137 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7332 (m170) REVERT: B 142 GLU cc_start: 0.7725 (pt0) cc_final: 0.7184 (pt0) REVERT: B 145 ILE cc_start: 0.8109 (mt) cc_final: 0.7852 (mm) REVERT: B 150 LEU cc_start: 0.8339 (tp) cc_final: 0.8104 (tp) REVERT: B 151 LYS cc_start: 0.7854 (mttm) cc_final: 0.7553 (tttm) REVERT: B 174 MET cc_start: 0.6729 (mtp) cc_final: 0.6311 (mtp) REVERT: B 183 MET cc_start: 0.6798 (mmm) cc_final: 0.6359 (mmm) REVERT: B 190 MET cc_start: 0.7693 (tpp) cc_final: 0.7297 (tpp) REVERT: B 247 GLU cc_start: 0.6181 (mp0) cc_final: 0.5616 (mp0) REVERT: B 266 PHE cc_start: 0.7316 (t80) cc_final: 0.6768 (t80) REVERT: B 306 ILE cc_start: 0.7944 (tt) cc_final: 0.7552 (pt) REVERT: B 354 LYS cc_start: 0.7470 (mmtp) cc_final: 0.6869 (mmtp) REVERT: B 380 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5837 (p90) REVERT: B 470 TRP cc_start: 0.8188 (p90) cc_final: 0.7963 (p90) REVERT: B 501 LYS cc_start: 0.7882 (tttt) cc_final: 0.7476 (tttt) REVERT: B 527 PHE cc_start: 0.6901 (p90) cc_final: 0.6420 (p90) REVERT: B 530 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8222 (ttmt) REVERT: B 532 LYS cc_start: 0.7597 (tttm) cc_final: 0.7216 (tttm) REVERT: B 533 LEU cc_start: 0.7728 (tp) cc_final: 0.7343 (tp) REVERT: B 536 LYS cc_start: 0.8101 (ttpp) cc_final: 0.7730 (ttpp) REVERT: B 551 MET cc_start: 0.5682 (mmt) cc_final: 0.4883 (tpp) REVERT: E 45 PHE cc_start: 0.7397 (t80) cc_final: 0.6836 (t80) REVERT: E 46 ASN cc_start: 0.7432 (t0) cc_final: 0.7134 (t0) REVERT: E 121 PHE cc_start: 0.7691 (m-80) cc_final: 0.6920 (m-10) REVERT: E 190 MET cc_start: 0.5712 (mtm) cc_final: 0.5261 (mtm) REVERT: E 282 ASN cc_start: 0.6731 (OUTLIER) cc_final: 0.5953 (t0) REVERT: E 378 TYR cc_start: 0.7133 (m-80) cc_final: 0.6424 (m-80) REVERT: E 398 PHE cc_start: 0.7840 (p90) cc_final: 0.7468 (p90) REVERT: E 455 THR cc_start: 0.4233 (p) cc_final: 0.3690 (m) REVERT: E 527 PHE cc_start: 0.7415 (p90) cc_final: 0.7160 (p90) REVERT: E 528 TRP cc_start: 0.6764 (m100) cc_final: 0.6442 (m100) REVERT: E 535 PHE cc_start: 0.7569 (m-80) cc_final: 0.7091 (m-80) REVERT: E 561 TYR cc_start: 0.8350 (m-80) cc_final: 0.7631 (m-80) REVERT: I 47 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7357 (t0) REVERT: I 52 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7437 (ttmm) REVERT: I 53 PHE cc_start: 0.7941 (m-80) cc_final: 0.7541 (m-80) REVERT: I 60 GLU cc_start: 0.7447 (tt0) cc_final: 0.7164 (tt0) REVERT: I 73 MET cc_start: 0.6170 (ptt) cc_final: 0.5949 (ptt) REVERT: I 87 MET cc_start: 0.6789 (ttp) cc_final: 0.6383 (ttp) REVERT: I 115 ASN cc_start: 0.7505 (t0) cc_final: 0.7056 (t0) REVERT: I 142 GLU cc_start: 0.7530 (pt0) cc_final: 0.7299 (pt0) REVERT: I 144 GLU cc_start: 0.7326 (pt0) cc_final: 0.7032 (pt0) REVERT: I 174 MET cc_start: 0.7090 (mtp) cc_final: 0.6672 (mtp) REVERT: I 268 PHE cc_start: 0.7763 (m-80) cc_final: 0.7382 (m-80) REVERT: I 319 MET cc_start: 0.5527 (tpp) cc_final: 0.5014 (tpp) REVERT: I 331 MET cc_start: 0.7227 (ttm) cc_final: 0.6967 (ttm) REVERT: I 383 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: I 387 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8194 (ttmm) REVERT: I 396 GLU cc_start: 0.7567 (tt0) cc_final: 0.7054 (tt0) REVERT: I 444 TYR cc_start: 0.7955 (p90) cc_final: 0.7609 (p90) REVERT: I 468 GLN cc_start: 0.7405 (mm110) cc_final: 0.7082 (mm110) REVERT: I 535 PHE cc_start: 0.8351 (m-80) cc_final: 0.7879 (m-80) REVERT: I 538 LYS cc_start: 0.8151 (tttp) cc_final: 0.7889 (ttmm) REVERT: I 539 LEU cc_start: 0.8654 (mt) cc_final: 0.8358 (mp) REVERT: I 544 THR cc_start: 0.7901 (p) cc_final: 0.7671 (p) REVERT: I 546 ASN cc_start: 0.7950 (p0) cc_final: 0.7688 (p0) REVERT: I 549 GLN cc_start: 0.8084 (tt0) cc_final: 0.7654 (tt0) REVERT: I 550 GLN cc_start: 0.7508 (mt0) cc_final: 0.7300 (mm110) REVERT: I 573 TYR cc_start: 0.8345 (p90) cc_final: 0.7840 (p90) REVERT: I 575 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7758 (mtmm) REVERT: F 52 LYS cc_start: 0.7911 (ttmm) cc_final: 0.7412 (ttmm) REVERT: F 60 GLU cc_start: 0.7537 (tt0) cc_final: 0.7137 (tt0) REVERT: F 180 ASN cc_start: 0.7647 (t0) cc_final: 0.7256 (t0) REVERT: F 248 ASN cc_start: 0.7252 (m-40) cc_final: 0.6900 (t0) REVERT: F 266 PHE cc_start: 0.7679 (t80) cc_final: 0.7392 (t80) REVERT: F 273 CYS cc_start: 0.8104 (t) cc_final: 0.7773 (t) REVERT: F 275 LEU cc_start: 0.7571 (mp) cc_final: 0.7272 (mp) REVERT: F 276 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7362 (m) REVERT: F 280 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7526 (mm110) REVERT: F 327 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6834 (mm-30) REVERT: F 459 ASN cc_start: 0.8330 (t0) cc_final: 0.8052 (t0) REVERT: F 475 ASP cc_start: 0.7182 (t0) cc_final: 0.6502 (t0) REVERT: F 484 VAL cc_start: 0.8534 (m) cc_final: 0.8151 (p) REVERT: F 491 GLN cc_start: 0.7892 (mm110) cc_final: 0.7423 (mm110) REVERT: F 551 MET cc_start: 0.6411 (ttt) cc_final: 0.5986 (ttt) REVERT: C 174 MET cc_start: 0.7342 (mtp) cc_final: 0.6821 (mtp) REVERT: C 250 VAL cc_start: 0.7426 (t) cc_final: 0.7202 (t) outliers start: 117 outliers final: 88 residues processed: 798 average time/residue: 0.3758 time to fit residues: 462.4374 Evaluate side-chains 858 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 757 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 524 TYR Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain G residue 570 LYS Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 383 GLN Chi-restraints excluded: chain I residue 443 ASN Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 553 ILE Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 444 TYR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 50.0000 chunk 308 optimal weight: 40.0000 chunk 188 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 chunk 257 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN F 416 GLN F 497 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26519 Z= 0.213 Angle : 0.577 10.077 36251 Z= 0.291 Chirality : 0.042 0.176 3973 Planarity : 0.005 0.051 4735 Dihedral : 5.348 70.052 3509 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.44 % Allowed : 18.72 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.60 (0.15), residues: 2990 helix: 0.05 (0.51), residues: 94 sheet: -0.43 (0.19), residues: 773 loop : -0.37 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 545 HIS 0.007 0.001 HIS F 277 PHE 0.034 0.002 PHE A 353 TYR 0.034 0.002 TYR F 233 ARG 0.010 0.001 ARG I 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 773 time to evaluate : 2.706 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: G 59 VAL cc_start: 0.8783 (t) cc_final: 0.8424 (m) REVERT: G 60 GLU cc_start: 0.7084 (tt0) cc_final: 0.6824 (tt0) REVERT: G 125 ASP cc_start: 0.6614 (m-30) cc_final: 0.6398 (m-30) REVERT: G 142 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6694 (mm-30) REVERT: G 185 PHE cc_start: 0.8221 (t80) cc_final: 0.7964 (t80) REVERT: G 211 TYR cc_start: 0.8209 (m-80) cc_final: 0.7853 (m-80) REVERT: G 217 THR cc_start: 0.7737 (p) cc_final: 0.7338 (p) REVERT: G 239 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6788 (m-30) REVERT: G 271 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7760 (mtpp) REVERT: G 319 MET cc_start: 0.2489 (OUTLIER) cc_final: 0.2192 (ptm) REVERT: G 382 ARG cc_start: 0.5621 (mtm180) cc_final: 0.5094 (mtm180) REVERT: G 390 THR cc_start: 0.8629 (t) cc_final: 0.8382 (p) REVERT: G 409 TYR cc_start: 0.8093 (t80) cc_final: 0.7734 (t80) REVERT: G 471 ASP cc_start: 0.7326 (t0) cc_final: 0.7055 (t0) REVERT: G 473 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6669 (tm-30) REVERT: G 536 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7756 (ttpp) REVERT: G 559 PHE cc_start: 0.7943 (m-80) cc_final: 0.7614 (m-80) REVERT: G 560 ASN cc_start: 0.7875 (m-40) cc_final: 0.7452 (m-40) REVERT: A 56 ASN cc_start: 0.7401 (m110) cc_final: 0.7164 (m110) REVERT: A 66 SER cc_start: 0.7494 (m) cc_final: 0.6991 (m) REVERT: A 92 VAL cc_start: 0.8433 (t) cc_final: 0.8170 (p) REVERT: A 99 ASP cc_start: 0.7071 (t70) cc_final: 0.6854 (t70) REVERT: A 100 ASP cc_start: 0.6788 (m-30) cc_final: 0.6321 (m-30) REVERT: A 142 GLU cc_start: 0.7426 (pt0) cc_final: 0.6922 (pt0) REVERT: A 174 MET cc_start: 0.7397 (mtp) cc_final: 0.6743 (mtp) REVERT: A 183 MET cc_start: 0.7114 (mmm) cc_final: 0.6703 (mmm) REVERT: A 211 TYR cc_start: 0.7271 (m-80) cc_final: 0.6948 (m-80) REVERT: A 218 LEU cc_start: 0.8299 (tp) cc_final: 0.7885 (tt) REVERT: A 313 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7883 (mtt-85) REVERT: A 344 SER cc_start: 0.8238 (t) cc_final: 0.7835 (p) REVERT: A 346 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6890 (mp0) REVERT: A 433 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7970 (p) REVERT: A 475 ASP cc_start: 0.7456 (t70) cc_final: 0.6658 (t0) REVERT: A 530 LYS cc_start: 0.7343 (ttmt) cc_final: 0.6897 (ttpp) REVERT: A 569 MET cc_start: 0.5585 (mmm) cc_final: 0.5324 (mmm) REVERT: A 574 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6312 (mm-30) REVERT: A 575 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7906 (mtpt) REVERT: B 80 ARG cc_start: 0.7154 (mtt-85) cc_final: 0.6491 (mtt-85) REVERT: B 101 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7914 (pt) REVERT: B 117 TRP cc_start: 0.6978 (m100) cc_final: 0.6461 (m100) REVERT: B 125 ASP cc_start: 0.7947 (m-30) cc_final: 0.7507 (m-30) REVERT: B 137 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.7207 (m170) REVERT: B 142 GLU cc_start: 0.7652 (pt0) cc_final: 0.7105 (pt0) REVERT: B 145 ILE cc_start: 0.8065 (mt) cc_final: 0.7663 (mm) REVERT: B 150 LEU cc_start: 0.8324 (tp) cc_final: 0.8074 (tp) REVERT: B 151 LYS cc_start: 0.7811 (mttm) cc_final: 0.7528 (tttm) REVERT: B 174 MET cc_start: 0.6720 (mtp) cc_final: 0.6328 (mtp) REVERT: B 183 MET cc_start: 0.6797 (mmm) cc_final: 0.6423 (mmm) REVERT: B 190 MET cc_start: 0.7650 (tpp) cc_final: 0.7255 (tpp) REVERT: B 247 GLU cc_start: 0.6184 (mp0) cc_final: 0.5599 (mp0) REVERT: B 266 PHE cc_start: 0.7362 (t80) cc_final: 0.6744 (t80) REVERT: B 306 ILE cc_start: 0.7965 (tt) cc_final: 0.7585 (pt) REVERT: B 354 LYS cc_start: 0.7476 (mmtp) cc_final: 0.6870 (mmtp) REVERT: B 380 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5636 (p90) REVERT: B 396 GLU cc_start: 0.7419 (tt0) cc_final: 0.7027 (tt0) REVERT: B 470 TRP cc_start: 0.8149 (p90) cc_final: 0.7934 (p90) REVERT: B 501 LYS cc_start: 0.7919 (tttt) cc_final: 0.7540 (tttt) REVERT: B 527 PHE cc_start: 0.6847 (p90) cc_final: 0.6289 (p90) REVERT: B 530 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8204 (ttmt) REVERT: B 532 LYS cc_start: 0.7560 (tttm) cc_final: 0.7179 (tttm) REVERT: B 533 LEU cc_start: 0.7736 (tp) cc_final: 0.7396 (tp) REVERT: B 536 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7750 (ttpp) REVERT: B 551 MET cc_start: 0.5661 (mmt) cc_final: 0.5327 (mmt) REVERT: E 45 PHE cc_start: 0.7353 (t80) cc_final: 0.6788 (t80) REVERT: E 46 ASN cc_start: 0.7486 (t0) cc_final: 0.7214 (t0) REVERT: E 121 PHE cc_start: 0.7643 (m-80) cc_final: 0.6912 (m-10) REVERT: E 190 MET cc_start: 0.5680 (mtm) cc_final: 0.5216 (mtm) REVERT: E 282 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.5935 (t0) REVERT: E 378 TYR cc_start: 0.7103 (m-80) cc_final: 0.6375 (m-80) REVERT: E 398 PHE cc_start: 0.7753 (p90) cc_final: 0.7369 (p90) REVERT: E 455 THR cc_start: 0.4247 (p) cc_final: 0.3747 (m) REVERT: E 527 PHE cc_start: 0.7391 (p90) cc_final: 0.7142 (p90) REVERT: E 528 TRP cc_start: 0.6717 (m100) cc_final: 0.6389 (m100) REVERT: E 535 PHE cc_start: 0.7581 (m-80) cc_final: 0.7110 (m-80) REVERT: E 561 TYR cc_start: 0.8369 (m-80) cc_final: 0.7675 (m-80) REVERT: I 47 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7252 (t0) REVERT: I 52 LYS cc_start: 0.7759 (ttmm) cc_final: 0.7464 (ttmm) REVERT: I 53 PHE cc_start: 0.7866 (m-80) cc_final: 0.7453 (m-80) REVERT: I 60 GLU cc_start: 0.7399 (tt0) cc_final: 0.7078 (tt0) REVERT: I 87 MET cc_start: 0.6769 (ttp) cc_final: 0.6357 (ttp) REVERT: I 115 ASN cc_start: 0.7442 (t0) cc_final: 0.7165 (t0) REVERT: I 142 GLU cc_start: 0.7489 (pt0) cc_final: 0.7267 (pt0) REVERT: I 144 GLU cc_start: 0.7298 (pt0) cc_final: 0.7018 (pt0) REVERT: I 174 MET cc_start: 0.7097 (mtp) cc_final: 0.6666 (mtp) REVERT: I 198 TYR cc_start: 0.7723 (m-80) cc_final: 0.7297 (m-80) REVERT: I 268 PHE cc_start: 0.7662 (m-80) cc_final: 0.7289 (m-80) REVERT: I 319 MET cc_start: 0.5631 (tpp) cc_final: 0.5207 (tpp) REVERT: I 331 MET cc_start: 0.7234 (ttm) cc_final: 0.6972 (ttm) REVERT: I 387 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8151 (ttmm) REVERT: I 396 GLU cc_start: 0.7529 (tt0) cc_final: 0.6972 (tt0) REVERT: I 444 TYR cc_start: 0.8003 (p90) cc_final: 0.7687 (p90) REVERT: I 535 PHE cc_start: 0.8355 (m-80) cc_final: 0.7880 (m-80) REVERT: I 538 LYS cc_start: 0.8114 (tttp) cc_final: 0.7861 (ttmm) REVERT: I 539 LEU cc_start: 0.8607 (mt) cc_final: 0.8340 (mp) REVERT: I 544 THR cc_start: 0.7894 (p) cc_final: 0.7661 (p) REVERT: I 546 ASN cc_start: 0.7947 (p0) cc_final: 0.7713 (p0) REVERT: I 573 TYR cc_start: 0.8554 (p90) cc_final: 0.8205 (p90) REVERT: I 575 LYS cc_start: 0.7870 (mtmm) cc_final: 0.6819 (mtmm) REVERT: F 52 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7388 (ttmm) REVERT: F 60 GLU cc_start: 0.7507 (tt0) cc_final: 0.7069 (tt0) REVERT: F 180 ASN cc_start: 0.7610 (t0) cc_final: 0.7220 (t0) REVERT: F 201 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8278 (mtpt) REVERT: F 242 GLN cc_start: 0.7396 (mt0) cc_final: 0.7067 (mt0) REVERT: F 248 ASN cc_start: 0.7202 (m-40) cc_final: 0.6898 (t0) REVERT: F 266 PHE cc_start: 0.7597 (t80) cc_final: 0.7379 (t80) REVERT: F 275 LEU cc_start: 0.7518 (mp) cc_final: 0.7255 (mp) REVERT: F 276 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7239 (m) REVERT: F 280 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7405 (mm110) REVERT: F 327 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6713 (mm-30) REVERT: F 330 ILE cc_start: 0.8747 (tt) cc_final: 0.8146 (tt) REVERT: F 468 GLN cc_start: 0.6188 (tt0) cc_final: 0.5983 (tt0) REVERT: F 475 ASP cc_start: 0.7140 (t0) cc_final: 0.6460 (t0) REVERT: F 484 VAL cc_start: 0.8460 (m) cc_final: 0.8061 (p) REVERT: F 491 GLN cc_start: 0.7797 (mm110) cc_final: 0.7446 (mm110) REVERT: F 551 MET cc_start: 0.6350 (ttt) cc_final: 0.5914 (ttt) REVERT: F 569 MET cc_start: 0.5654 (mmm) cc_final: 0.5342 (mmm) REVERT: F 582 LYS cc_start: 0.7601 (mtpp) cc_final: 0.7056 (mtpp) REVERT: C 174 MET cc_start: 0.7350 (mtp) cc_final: 0.6830 (mtp) REVERT: C 250 VAL cc_start: 0.7415 (t) cc_final: 0.7194 (t) outliers start: 94 outliers final: 68 residues processed: 798 average time/residue: 0.3771 time to fit residues: 463.6199 Evaluate side-chains 843 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 764 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 570 LYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 443 ASN Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 553 ILE Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 50.0000 chunk 274 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 258 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 265 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 181 ASN ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.217069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159995 restraints weight = 40853.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.165796 restraints weight = 17552.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.169434 restraints weight = 10254.420| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.278 26519 Z= 0.396 Angle : 0.814 59.194 36251 Z= 0.462 Chirality : 0.045 0.356 3973 Planarity : 0.005 0.098 4735 Dihedral : 5.384 69.987 3509 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.55 % Allowed : 19.16 % Favored : 77.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 2990 helix: -0.01 (0.50), residues: 94 sheet: -0.41 (0.19), residues: 771 loop : -0.38 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 545 HIS 0.008 0.001 HIS F 277 PHE 0.047 0.002 PHE F 141 TYR 0.030 0.002 TYR F 233 ARG 0.021 0.001 ARG F 332 =============================================================================== Job complete usr+sys time: 7603.41 seconds wall clock time: 134 minutes 43.32 seconds (8083.32 seconds total)