Starting phenix.real_space_refine on Sat Mar 16 23:40:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/03_2024/8igg_35432.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/03_2024/8igg_35432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/03_2024/8igg_35432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/03_2024/8igg_35432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/03_2024/8igg_35432.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/03_2024/8igg_35432.pdb" } resolution = 4.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 50 5.16 5 C 10002 2.51 5 N 2892 2.21 5 O 3054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 300": "OE1" <-> "OE2" Residue "E ASP 437": "OD1" <-> "OD2" Residue "E TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C ASP 495": "OD1" <-> "OD2" Residue "C TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15998 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4014 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3985 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 23, 'TRANS': 487} Chain breaks: 3 Chain: "B" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4014 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3985 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 23, 'TRANS': 487} Chain breaks: 3 Time building chain proxies: 8.51, per 1000 atoms: 0.53 Number of scatterers: 15998 At special positions: 0 Unit cell: (148.75, 126.25, 87.5, 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 50 16.00 O 3054 8.00 N 2892 7.00 C 10002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.25 Conformation dependent library (CDL) restraints added in 2.8 seconds 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 22 sheets defined 42.2% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.908A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 55 " --> pdb=" O ASN E 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 55' Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.826A pdb=" N GLU E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.846A pdb=" N HIS E 101 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 102' Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.513A pdb=" N ASP E 201 " --> pdb=" O VAL E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 202 through 226 Processing helix chain 'E' and resid 231 through 235 Processing helix chain 'E' and resid 302 through 311 removed outlier: 3.892A pdb=" N GLN E 306 " --> pdb=" O THR E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 352 through 367 removed outlier: 4.432A pdb=" N SER E 356 " --> pdb=" O ALA E 353 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY E 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TRP E 362 " --> pdb=" O GLY E 359 " (cutoff:3.500A) Proline residue: E 365 - end of helix Processing helix chain 'E' and resid 378 through 384 removed outlier: 3.565A pdb=" N ALA E 381 " --> pdb=" O ASP E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 410 Processing helix chain 'E' and resid 428 through 439 removed outlier: 3.848A pdb=" N LEU E 434 " --> pdb=" O GLN E 430 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 435 " --> pdb=" O MET E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 460 Processing helix chain 'E' and resid 462 through 466 Processing helix chain 'E' and resid 497 through 499 No H-bonds generated for 'chain 'E' and resid 497 through 499' Processing helix chain 'E' and resid 501 through 509 Processing helix chain 'E' and resid 511 through 523 Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 560 through 576 removed outlier: 3.656A pdb=" N ILE E 564 " --> pdb=" O ASN E 560 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG E 569 " --> pdb=" O GLU E 565 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU E 576 " --> pdb=" O ALA E 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.616A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 202 through 222 removed outlier: 3.546A pdb=" N LEU A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.245A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 237' Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.546A pdb=" N PHE A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.866A pdb=" N ALA A 361 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TRP A 362 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 4.031A pdb=" N ALA A 381 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 428 through 439 removed outlier: 4.804A pdb=" N LEU A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.983A pdb=" N PHE A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.614A pdb=" N LEU A 499 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 528 through 544 removed outlier: 3.684A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 removed outlier: 3.753A pdb=" N ILE A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.618A pdb=" N ASN A 601 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.908A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.826A pdb=" N GLU B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.846A pdb=" N HIS B 101 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 102 " --> pdb=" O ASP B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 163 through 179 Processing helix chain 'B' and resid 198 through 201 removed outlier: 3.513A pdb=" N ASP B 201 " --> pdb=" O VAL B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 202 through 226 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 302 through 311 removed outlier: 3.892A pdb=" N GLN B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 4.432A pdb=" N SER B 356 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TRP B 362 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.565A pdb=" N ALA B 381 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.848A pdb=" N LEU B 434 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 501 through 509 Processing helix chain 'B' and resid 511 through 523 Processing helix chain 'B' and resid 528 through 543 Processing helix chain 'B' and resid 560 through 576 removed outlier: 3.656A pdb=" N ILE B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 82 Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.616A pdb=" N PHE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 202 through 222 removed outlier: 3.546A pdb=" N LEU C 221 " --> pdb=" O CYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.245A pdb=" N LYS C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 237' Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.546A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 removed outlier: 3.866A pdb=" N ALA C 361 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TRP C 362 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 removed outlier: 4.031A pdb=" N ALA C 381 " --> pdb=" O ASP C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 412 Processing helix chain 'C' and resid 428 through 439 removed outlier: 4.804A pdb=" N LEU C 434 " --> pdb=" O GLN C 430 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C 435 " --> pdb=" O MET C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 457 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.983A pdb=" N PHE C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 499 removed outlier: 3.614A pdb=" N LEU C 499 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 514 through 523 Processing helix chain 'C' and resid 528 through 544 removed outlier: 3.684A pdb=" N ARG C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 3.753A pdb=" N ILE C 564 " --> pdb=" O ASN C 560 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 601 removed outlier: 3.618A pdb=" N ASN C 601 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'E' and resid 92 through 93 removed outlier: 9.018A pdb=" N PHE E 191 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 139 through 145 Processing sheet with id=AA4, first strand: chain 'E' and resid 248 through 249 removed outlier: 6.858A pdb=" N ILE E 266 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA E 294 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 268 " --> pdb=" O GLN E 292 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 292 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR E 270 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA E 294 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP E 331 " --> pdb=" O ASP E 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN E 423 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE E 418 " --> pdb=" O TYR E 559 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR E 550 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN E 486 " --> pdb=" O TYR E 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY E 552 " --> pdb=" O LEU E 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 475 through 476 removed outlier: 5.175A pdb=" N PHE E 418 " --> pdb=" O TYR E 559 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP E 331 " --> pdb=" O ASP E 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN E 423 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA E 294 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR E 270 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 292 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 268 " --> pdb=" O GLN E 292 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA E 294 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E 266 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU E 243 " --> pdb=" O THR E 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 96 removed outlier: 4.116A pdb=" N SER A 106 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 127 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE A 191 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR A 242 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 272 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS A 289 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP A 323 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL A 417 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA A 325 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN A 419 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 327 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 421 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A 329 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN A 423 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP A 331 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR A 242 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 272 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS A 289 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP A 323 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL A 417 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA A 325 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN A 419 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 327 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 421 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A 329 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN A 423 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP A 331 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 484 " --> pdb=" O THR A 551 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AB3, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AB4, first strand: chain 'B' and resid 92 through 93 removed outlier: 9.018A pdb=" N PHE B 191 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 139 through 145 Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 249 removed outlier: 6.858A pdb=" N ILE B 266 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 294 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 268 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 292 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 270 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 294 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP B 331 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN B 423 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE B 418 " --> pdb=" O TYR B 559 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR B 550 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN B 486 " --> pdb=" O TYR B 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 552 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 475 through 476 removed outlier: 5.175A pdb=" N PHE B 418 " --> pdb=" O TYR B 559 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP B 331 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN B 423 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 294 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 270 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 292 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 268 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 294 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 266 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 243 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB9, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=AC1, first strand: chain 'C' and resid 92 through 96 removed outlier: 4.116A pdb=" N SER C 106 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 127 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 191 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR C 242 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 272 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 289 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 294 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP C 323 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL C 417 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 325 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN C 419 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 327 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP C 421 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE C 329 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN C 423 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP C 331 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C 418 " --> pdb=" O TYR C 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR C 242 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 272 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 289 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 294 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP C 323 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL C 417 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 325 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN C 419 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 327 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP C 421 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE C 329 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN C 423 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP C 331 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C 418 " --> pdb=" O TYR C 559 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 484 " --> pdb=" O THR C 551 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 254 through 255 814 hydrogen bonds defined for protein. 2184 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: 5.13 Time building geometry restraints manager: 6.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4776 1.33 - 1.45: 2534 1.45 - 1.57: 8892 1.57 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 16294 Sorted by residual: bond pdb=" N VAL A 412 " pdb=" CA VAL A 412 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N VAL C 412 " pdb=" CA VAL C 412 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N GLN C 411 " pdb=" CA GLN C 411 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.22e-02 6.72e+03 9.96e+00 bond pdb=" N GLN A 411 " pdb=" CA GLN A 411 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.22e-02 6.72e+03 9.96e+00 bond pdb=" N MET A 408 " pdb=" CA MET A 408 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.53e+00 ... (remaining 16289 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.58: 454 106.58 - 113.45: 8746 113.45 - 120.33: 5812 120.33 - 127.21: 6920 127.21 - 134.08: 174 Bond angle restraints: 22106 Sorted by residual: angle pdb=" N GLN A 411 " pdb=" CA GLN A 411 " pdb=" C GLN A 411 " ideal model delta sigma weight residual 111.56 118.29 -6.73 1.53e+00 4.27e-01 1.93e+01 angle pdb=" N GLN C 411 " pdb=" CA GLN C 411 " pdb=" C GLN C 411 " ideal model delta sigma weight residual 111.56 118.29 -6.73 1.53e+00 4.27e-01 1.93e+01 angle pdb=" CA GLN C 411 " pdb=" C GLN C 411 " pdb=" O GLN C 411 " ideal model delta sigma weight residual 120.56 116.00 4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" CA GLN A 411 " pdb=" C GLN A 411 " pdb=" O GLN A 411 " ideal model delta sigma weight residual 120.56 116.00 4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" N GLN C 406 " pdb=" CA GLN C 406 " pdb=" C GLN C 406 " ideal model delta sigma weight residual 111.03 107.03 4.00 1.11e+00 8.12e-01 1.30e+01 ... (remaining 22101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8750 17.93 - 35.86: 852 35.86 - 53.79: 142 53.79 - 71.72: 32 71.72 - 89.65: 30 Dihedral angle restraints: 9806 sinusoidal: 3928 harmonic: 5878 Sorted by residual: dihedral pdb=" CB GLU E 573 " pdb=" CG GLU E 573 " pdb=" CD GLU E 573 " pdb=" OE1 GLU E 573 " ideal model delta sinusoidal sigma weight residual 0.00 -89.52 89.52 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 573 " pdb=" CG GLU B 573 " pdb=" CD GLU B 573 " pdb=" OE1 GLU B 573 " ideal model delta sinusoidal sigma weight residual 0.00 -89.52 89.52 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 76 " pdb=" CD ARG B 76 " pdb=" NE ARG B 76 " pdb=" CZ ARG B 76 " ideal model delta sinusoidal sigma weight residual -90.00 -134.44 44.44 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 9803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1816 0.040 - 0.081: 426 0.081 - 0.121: 176 0.121 - 0.161: 24 0.161 - 0.202: 10 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA GLN C 406 " pdb=" N GLN C 406 " pdb=" C GLN C 406 " pdb=" CB GLN C 406 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN A 406 " pdb=" N GLN A 406 " pdb=" C GLN A 406 " pdb=" CB GLN A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN A 411 " pdb=" N GLN A 411 " pdb=" C GLN A 411 " pdb=" CB GLN A 411 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 2449 not shown) Planarity restraints: 2970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 405 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY A 405 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY A 405 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN A 406 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 405 " -0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY C 405 " 0.078 2.00e-02 2.50e+03 pdb=" O GLY C 405 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN C 406 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 367 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO E 368 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 368 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 368 " -0.024 5.00e-02 4.00e+02 ... (remaining 2967 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 440 2.70 - 3.25: 16556 3.25 - 3.80: 24249 3.80 - 4.35: 30313 4.35 - 4.90: 49078 Nonbonded interactions: 120636 Sorted by model distance: nonbonded pdb=" O ASP B 581 " pdb=" OD1 ASN B 582 " model vdw 2.146 3.040 nonbonded pdb=" O ASP E 581 " pdb=" OD1 ASN E 582 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR A 270 " pdb=" OD1 ASN A 291 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR C 270 " pdb=" OD1 ASN C 291 " model vdw 2.195 2.440 nonbonded pdb=" OD1 ASN A 595 " pdb=" OH TYR B 519 " model vdw 2.209 2.440 ... (remaining 120631 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 63 through 273 or resid 287 through 369 or (resid 370 and \ (name N or name CA or name C or name O or name CB )) or resid 371 through 582)) selection = (chain 'B' and (resid 63 through 137 or resid 155 through 303 or resid 320 throu \ gh 582)) selection = (chain 'C' and (resid 63 through 273 or resid 287 through 369 or (resid 370 and \ (name N or name CA or name C or name O or name CB )) or resid 371 through 582)) selection = (chain 'E' and (resid 63 through 137 or resid 155 through 303 or resid 320 throu \ gh 582)) } 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.290 Check model and map are aligned: 0.250 Set scattering table: 0.190 Process input model: 43.540 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.003 0.041 16294 Z= 0.164 Angle : 0.611 9.230 22106 Z= 0.319 Chirality : 0.043 0.202 2452 Planarity : 0.003 0.045 2970 Dihedral : 15.139 89.654 6006 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 2026 helix: 1.05 (0.20), residues: 714 sheet: -0.24 (0.27), residues: 392 loop : -0.79 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 487 HIS 0.002 0.001 HIS C 101 PHE 0.018 0.001 PHE C 404 TYR 0.014 0.001 TYR C 570 ARG 0.005 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 LEU cc_start: 0.9502 (mp) cc_final: 0.9247 (mt) REVERT: E 436 LEU cc_start: 0.8781 (mp) cc_final: 0.8565 (mt) REVERT: E 505 LEU cc_start: 0.8814 (tp) cc_final: 0.8497 (tp) REVERT: A 256 ASP cc_start: 0.7632 (p0) cc_final: 0.7379 (p0) REVERT: A 432 ASP cc_start: 0.7885 (m-30) cc_final: 0.7354 (m-30) REVERT: B 129 LEU cc_start: 0.9502 (mp) cc_final: 0.9246 (mt) REVERT: B 436 LEU cc_start: 0.8779 (mp) cc_final: 0.8565 (mt) REVERT: B 505 LEU cc_start: 0.8814 (tp) cc_final: 0.8499 (tp) REVERT: C 256 ASP cc_start: 0.7634 (p0) cc_final: 0.7381 (p0) REVERT: C 432 ASP cc_start: 0.7881 (m-30) cc_final: 0.7350 (m-30) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2433 time to fit residues: 132.0926 Evaluate side-chains 272 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 313 ASN A 411 GLN A 413 GLN A 472 GLN B 313 ASN C 411 GLN C 413 GLN C 445 GLN C 472 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16294 Z= 0.229 Angle : 0.563 8.047 22106 Z= 0.282 Chirality : 0.043 0.171 2452 Planarity : 0.004 0.043 2970 Dihedral : 3.807 14.359 2208 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 2026 helix: 1.06 (0.20), residues: 732 sheet: -0.39 (0.27), residues: 402 loop : -0.71 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 487 HIS 0.003 0.001 HIS C 255 PHE 0.011 0.001 PHE E 296 TYR 0.016 0.001 TYR B 559 ARG 0.004 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 318 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 295 MET cc_start: 0.8024 (ptt) cc_final: 0.7778 (ptt) REVERT: E 384 TRP cc_start: 0.8372 (m100) cc_final: 0.7693 (m100) REVERT: E 505 LEU cc_start: 0.8871 (tp) cc_final: 0.8559 (tp) REVERT: A 256 ASP cc_start: 0.7724 (p0) cc_final: 0.7336 (p0) REVERT: A 408 MET cc_start: 0.9166 (tpp) cc_final: 0.8280 (tpp) REVERT: A 432 ASP cc_start: 0.8014 (m-30) cc_final: 0.7579 (m-30) REVERT: B 295 MET cc_start: 0.8025 (ptt) cc_final: 0.7775 (ptt) REVERT: B 384 TRP cc_start: 0.8372 (m100) cc_final: 0.7696 (m100) REVERT: B 505 LEU cc_start: 0.8872 (tp) cc_final: 0.8559 (tp) REVERT: C 256 ASP cc_start: 0.7723 (p0) cc_final: 0.7335 (p0) REVERT: C 408 MET cc_start: 0.9166 (tpp) cc_final: 0.8275 (tpp) REVERT: C 432 ASP cc_start: 0.8013 (m-30) cc_final: 0.7580 (m-30) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.2416 time to fit residues: 118.3239 Evaluate side-chains 255 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 445 GLN A 472 GLN ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 472 GLN ** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16294 Z= 0.181 Angle : 0.542 8.846 22106 Z= 0.269 Chirality : 0.042 0.162 2452 Planarity : 0.003 0.042 2970 Dihedral : 3.748 13.795 2208 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 2026 helix: 1.15 (0.20), residues: 732 sheet: -0.32 (0.26), residues: 402 loop : -0.79 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 487 HIS 0.002 0.001 HIS B 101 PHE 0.010 0.001 PHE B 296 TYR 0.016 0.001 TYR A 543 ARG 0.003 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7603 (mt0) REVERT: E 384 TRP cc_start: 0.8358 (m100) cc_final: 0.7672 (m100) REVERT: E 425 MET cc_start: 0.8553 (tpp) cc_final: 0.7752 (mpp) REVERT: E 505 LEU cc_start: 0.8877 (tp) cc_final: 0.8541 (tp) REVERT: A 256 ASP cc_start: 0.7708 (p0) cc_final: 0.7272 (p0) REVERT: A 280 GLU cc_start: 0.6897 (pt0) cc_final: 0.6290 (pt0) REVERT: A 408 MET cc_start: 0.9283 (tpp) cc_final: 0.8593 (tpp) REVERT: A 412 VAL cc_start: 0.9280 (t) cc_final: 0.9003 (m) REVERT: A 432 ASP cc_start: 0.8009 (m-30) cc_final: 0.7734 (m-30) REVERT: A 492 GLU cc_start: 0.7518 (pm20) cc_final: 0.6584 (pm20) REVERT: B 314 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7601 (mt0) REVERT: B 384 TRP cc_start: 0.8358 (m100) cc_final: 0.7674 (m100) REVERT: B 425 MET cc_start: 0.8552 (tpp) cc_final: 0.7750 (mpp) REVERT: B 505 LEU cc_start: 0.8879 (tp) cc_final: 0.8543 (tp) REVERT: C 256 ASP cc_start: 0.7710 (p0) cc_final: 0.7271 (p0) REVERT: C 280 GLU cc_start: 0.6898 (pt0) cc_final: 0.6288 (pt0) REVERT: C 408 MET cc_start: 0.9283 (tpp) cc_final: 0.8594 (tpp) REVERT: C 412 VAL cc_start: 0.9279 (t) cc_final: 0.9002 (m) REVERT: C 432 ASP cc_start: 0.8008 (m-30) cc_final: 0.7733 (m-30) REVERT: C 492 GLU cc_start: 0.7519 (pm20) cc_final: 0.6586 (pm20) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2492 time to fit residues: 129.6806 Evaluate side-chains 268 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.6980 chunk 139 optimal weight: 0.0030 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 278 GLN A 472 GLN ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN C 117 ASN C 278 GLN C 472 GLN ** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16294 Z= 0.323 Angle : 0.613 9.168 22106 Z= 0.312 Chirality : 0.044 0.180 2452 Planarity : 0.004 0.044 2970 Dihedral : 4.139 15.093 2208 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 2026 helix: 0.86 (0.20), residues: 746 sheet: -0.66 (0.26), residues: 426 loop : -0.96 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 487 HIS 0.003 0.001 HIS A 224 PHE 0.022 0.002 PHE B 296 TYR 0.019 0.002 TYR C 570 ARG 0.003 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8445 (m100) cc_final: 0.7718 (m100) REVERT: E 505 LEU cc_start: 0.8841 (tp) cc_final: 0.8420 (tp) REVERT: A 218 ASP cc_start: 0.7978 (t70) cc_final: 0.7697 (t0) REVERT: A 256 ASP cc_start: 0.7716 (p0) cc_final: 0.7273 (p0) REVERT: A 408 MET cc_start: 0.9277 (tpp) cc_final: 0.8613 (tpp) REVERT: A 412 VAL cc_start: 0.9378 (t) cc_final: 0.9141 (m) REVERT: A 432 ASP cc_start: 0.7900 (m-30) cc_final: 0.7479 (m-30) REVERT: B 384 TRP cc_start: 0.8443 (m100) cc_final: 0.7717 (m100) REVERT: B 505 LEU cc_start: 0.8843 (tp) cc_final: 0.8422 (tp) REVERT: C 218 ASP cc_start: 0.7980 (t70) cc_final: 0.7696 (t0) REVERT: C 256 ASP cc_start: 0.7717 (p0) cc_final: 0.7272 (p0) REVERT: C 408 MET cc_start: 0.9278 (tpp) cc_final: 0.8614 (tpp) REVERT: C 412 VAL cc_start: 0.9380 (t) cc_final: 0.9141 (m) REVERT: C 432 ASP cc_start: 0.7901 (m-30) cc_final: 0.7480 (m-30) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2431 time to fit residues: 117.3069 Evaluate side-chains 271 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.0270 chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 GLN ** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16294 Z= 0.277 Angle : 0.598 8.711 22106 Z= 0.301 Chirality : 0.044 0.176 2452 Planarity : 0.004 0.043 2970 Dihedral : 4.128 14.430 2208 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2026 helix: 0.81 (0.20), residues: 746 sheet: -0.45 (0.26), residues: 402 loop : -1.14 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 487 HIS 0.003 0.001 HIS B 101 PHE 0.015 0.001 PHE A 167 TYR 0.018 0.002 TYR A 570 ARG 0.003 0.000 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8432 (m100) cc_final: 0.7671 (m100) REVERT: E 505 LEU cc_start: 0.8816 (tp) cc_final: 0.8344 (tp) REVERT: A 218 ASP cc_start: 0.7978 (t70) cc_final: 0.7689 (t0) REVERT: A 256 ASP cc_start: 0.7720 (p0) cc_final: 0.7274 (p0) REVERT: A 408 MET cc_start: 0.9271 (tpp) cc_final: 0.8551 (tpp) REVERT: A 412 VAL cc_start: 0.9372 (t) cc_final: 0.9135 (m) REVERT: A 432 ASP cc_start: 0.7924 (m-30) cc_final: 0.7562 (m-30) REVERT: A 492 GLU cc_start: 0.7671 (pm20) cc_final: 0.6776 (pm20) REVERT: B 384 TRP cc_start: 0.8433 (m100) cc_final: 0.7670 (m100) REVERT: B 505 LEU cc_start: 0.8817 (tp) cc_final: 0.8344 (tp) REVERT: C 218 ASP cc_start: 0.7980 (t70) cc_final: 0.7692 (t0) REVERT: C 256 ASP cc_start: 0.7721 (p0) cc_final: 0.7273 (p0) REVERT: C 408 MET cc_start: 0.9272 (tpp) cc_final: 0.8554 (tpp) REVERT: C 412 VAL cc_start: 0.9373 (t) cc_final: 0.9134 (m) REVERT: C 432 ASP cc_start: 0.7922 (m-30) cc_final: 0.7563 (m-30) REVERT: C 492 GLU cc_start: 0.7675 (pm20) cc_final: 0.6778 (pm20) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2504 time to fit residues: 124.4439 Evaluate side-chains 275 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 163 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN C 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16294 Z= 0.136 Angle : 0.561 8.214 22106 Z= 0.274 Chirality : 0.042 0.162 2452 Planarity : 0.003 0.042 2970 Dihedral : 3.756 14.499 2208 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 2026 helix: 1.06 (0.20), residues: 732 sheet: -0.40 (0.26), residues: 400 loop : -0.88 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 487 HIS 0.002 0.000 HIS C 101 PHE 0.009 0.001 PHE B 296 TYR 0.017 0.001 TYR A 570 ARG 0.002 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7652 (tp40) REVERT: E 384 TRP cc_start: 0.8300 (m100) cc_final: 0.7565 (m100) REVERT: E 425 MET cc_start: 0.8640 (tpp) cc_final: 0.7857 (tpp) REVERT: E 505 LEU cc_start: 0.8840 (tp) cc_final: 0.8379 (tp) REVERT: A 256 ASP cc_start: 0.7665 (p0) cc_final: 0.7202 (p0) REVERT: A 376 MET cc_start: 0.8143 (ptm) cc_final: 0.7916 (ptm) REVERT: A 408 MET cc_start: 0.9218 (tpp) cc_final: 0.8369 (tpp) REVERT: A 412 VAL cc_start: 0.9330 (t) cc_final: 0.9064 (m) REVERT: A 432 ASP cc_start: 0.7937 (m-30) cc_final: 0.7690 (m-30) REVERT: A 492 GLU cc_start: 0.7614 (pm20) cc_final: 0.6846 (pm20) REVERT: B 314 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7652 (tp40) REVERT: B 384 TRP cc_start: 0.8297 (m100) cc_final: 0.7564 (m100) REVERT: B 425 MET cc_start: 0.8641 (tpp) cc_final: 0.7856 (mpp) REVERT: B 505 LEU cc_start: 0.8878 (tp) cc_final: 0.8435 (tp) REVERT: C 256 ASP cc_start: 0.7666 (p0) cc_final: 0.7199 (p0) REVERT: C 376 MET cc_start: 0.8141 (ptm) cc_final: 0.7915 (ptm) REVERT: C 408 MET cc_start: 0.9218 (tpp) cc_final: 0.8368 (tpp) REVERT: C 412 VAL cc_start: 0.9328 (t) cc_final: 0.9061 (m) REVERT: C 432 ASP cc_start: 0.7939 (m-30) cc_final: 0.7665 (m-30) REVERT: C 492 GLU cc_start: 0.7615 (pm20) cc_final: 0.6847 (pm20) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2394 time to fit residues: 129.3525 Evaluate side-chains 280 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 9.9990 chunk 22 optimal weight: 0.0370 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 119 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16294 Z= 0.141 Angle : 0.554 8.193 22106 Z= 0.271 Chirality : 0.042 0.162 2452 Planarity : 0.003 0.042 2970 Dihedral : 3.690 15.614 2208 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 2026 helix: 1.13 (0.20), residues: 730 sheet: -0.26 (0.26), residues: 396 loop : -0.87 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 487 HIS 0.002 0.000 HIS A 101 PHE 0.011 0.001 PHE C 283 TYR 0.017 0.001 TYR C 570 ARG 0.003 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8343 (m100) cc_final: 0.7580 (m100) REVERT: E 505 LEU cc_start: 0.8858 (tp) cc_final: 0.8436 (tp) REVERT: A 256 ASP cc_start: 0.7713 (p0) cc_final: 0.7235 (p0) REVERT: A 408 MET cc_start: 0.9215 (tpp) cc_final: 0.8363 (tpp) REVERT: A 412 VAL cc_start: 0.9350 (t) cc_final: 0.9088 (m) REVERT: A 432 ASP cc_start: 0.8216 (m-30) cc_final: 0.7875 (m-30) REVERT: A 492 GLU cc_start: 0.7447 (pm20) cc_final: 0.6639 (pm20) REVERT: B 384 TRP cc_start: 0.8343 (m100) cc_final: 0.7580 (m100) REVERT: B 505 LEU cc_start: 0.8860 (tp) cc_final: 0.8438 (tp) REVERT: C 256 ASP cc_start: 0.7712 (p0) cc_final: 0.7234 (p0) REVERT: C 408 MET cc_start: 0.9215 (tpp) cc_final: 0.8365 (tpp) REVERT: C 412 VAL cc_start: 0.9349 (t) cc_final: 0.9087 (m) REVERT: C 432 ASP cc_start: 0.8218 (m-30) cc_final: 0.7876 (m-30) REVERT: C 492 GLU cc_start: 0.7452 (pm20) cc_final: 0.6690 (pm20) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2391 time to fit residues: 125.4549 Evaluate side-chains 273 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 0.0570 chunk 59 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 0.2980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 472 GLN C 101 HIS C 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16294 Z= 0.130 Angle : 0.552 9.188 22106 Z= 0.270 Chirality : 0.042 0.169 2452 Planarity : 0.003 0.042 2970 Dihedral : 3.634 15.972 2208 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 2026 helix: 1.20 (0.20), residues: 732 sheet: -0.19 (0.27), residues: 398 loop : -0.84 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 487 HIS 0.002 0.000 HIS C 101 PHE 0.011 0.001 PHE A 74 TYR 0.020 0.002 TYR C 346 ARG 0.002 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8290 (m100) cc_final: 0.7594 (m100) REVERT: E 425 MET cc_start: 0.8577 (tpp) cc_final: 0.7766 (tpp) REVERT: E 505 LEU cc_start: 0.8884 (tp) cc_final: 0.8463 (tp) REVERT: A 108 LEU cc_start: 0.9028 (tp) cc_final: 0.8815 (tt) REVERT: A 256 ASP cc_start: 0.7721 (p0) cc_final: 0.7301 (p0) REVERT: A 408 MET cc_start: 0.9151 (tpp) cc_final: 0.8804 (tpp) REVERT: B 384 TRP cc_start: 0.8288 (m100) cc_final: 0.7594 (m100) REVERT: B 425 MET cc_start: 0.8578 (tpp) cc_final: 0.7764 (tpp) REVERT: B 505 LEU cc_start: 0.8884 (tp) cc_final: 0.8463 (tp) REVERT: C 108 LEU cc_start: 0.9030 (tp) cc_final: 0.8825 (tt) REVERT: C 256 ASP cc_start: 0.7718 (p0) cc_final: 0.7301 (p0) REVERT: C 408 MET cc_start: 0.9150 (tpp) cc_final: 0.8802 (tpp) REVERT: C 432 ASP cc_start: 0.7711 (m-30) cc_final: 0.7345 (m-30) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2330 time to fit residues: 121.4156 Evaluate side-chains 262 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 358 HIS C 101 HIS C 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16294 Z= 0.136 Angle : 0.565 9.066 22106 Z= 0.272 Chirality : 0.042 0.169 2452 Planarity : 0.003 0.041 2970 Dihedral : 3.579 15.755 2208 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 2026 helix: 1.28 (0.20), residues: 732 sheet: -0.12 (0.27), residues: 398 loop : -0.83 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 487 HIS 0.007 0.001 HIS A 358 PHE 0.011 0.001 PHE C 283 TYR 0.019 0.001 TYR E 559 ARG 0.002 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8291 (m100) cc_final: 0.7601 (m100) REVERT: E 425 MET cc_start: 0.8556 (tpp) cc_final: 0.7771 (tpp) REVERT: E 505 LEU cc_start: 0.8885 (tp) cc_final: 0.8440 (tp) REVERT: A 218 ASP cc_start: 0.7873 (t70) cc_final: 0.7670 (t0) REVERT: A 256 ASP cc_start: 0.7733 (p0) cc_final: 0.7339 (p0) REVERT: A 408 MET cc_start: 0.9153 (tpp) cc_final: 0.8216 (tpp) REVERT: A 412 VAL cc_start: 0.9371 (t) cc_final: 0.9144 (m) REVERT: A 432 ASP cc_start: 0.7836 (m-30) cc_final: 0.7410 (m-30) REVERT: B 384 TRP cc_start: 0.8289 (m100) cc_final: 0.7601 (m100) REVERT: B 425 MET cc_start: 0.8558 (tpp) cc_final: 0.7762 (tpp) REVERT: B 505 LEU cc_start: 0.8886 (tp) cc_final: 0.8442 (tp) REVERT: C 218 ASP cc_start: 0.7871 (t70) cc_final: 0.7669 (t0) REVERT: C 256 ASP cc_start: 0.7731 (p0) cc_final: 0.7339 (p0) REVERT: C 408 MET cc_start: 0.9153 (tpp) cc_final: 0.8220 (tpp) REVERT: C 412 VAL cc_start: 0.9370 (t) cc_final: 0.9143 (m) REVERT: C 432 ASP cc_start: 0.7790 (m-30) cc_final: 0.7473 (m-30) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2514 time to fit residues: 125.2732 Evaluate side-chains 274 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16294 Z= 0.149 Angle : 0.578 11.078 22106 Z= 0.277 Chirality : 0.042 0.169 2452 Planarity : 0.003 0.042 2970 Dihedral : 3.541 15.589 2208 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 2026 helix: 1.32 (0.20), residues: 732 sheet: -0.13 (0.27), residues: 396 loop : -0.83 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 487 HIS 0.002 0.000 HIS B 101 PHE 0.013 0.001 PHE C 283 TYR 0.022 0.002 TYR E 559 ARG 0.002 0.000 ARG E 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 LEU cc_start: 0.9480 (mp) cc_final: 0.9074 (mt) REVERT: E 384 TRP cc_start: 0.8304 (m100) cc_final: 0.7598 (m100) REVERT: E 425 MET cc_start: 0.8549 (tpp) cc_final: 0.7762 (tpp) REVERT: E 505 LEU cc_start: 0.8858 (tp) cc_final: 0.8413 (tp) REVERT: A 218 ASP cc_start: 0.7886 (t70) cc_final: 0.7661 (t0) REVERT: A 256 ASP cc_start: 0.7676 (p0) cc_final: 0.7303 (p0) REVERT: A 408 MET cc_start: 0.9158 (tpp) cc_final: 0.8230 (tpp) REVERT: A 412 VAL cc_start: 0.9389 (t) cc_final: 0.9165 (m) REVERT: A 432 ASP cc_start: 0.7896 (m-30) cc_final: 0.7460 (m-30) REVERT: B 129 LEU cc_start: 0.9479 (mp) cc_final: 0.9076 (mt) REVERT: B 384 TRP cc_start: 0.8301 (m100) cc_final: 0.7596 (m100) REVERT: B 425 MET cc_start: 0.8550 (tpp) cc_final: 0.7768 (tpp) REVERT: B 505 LEU cc_start: 0.8858 (tp) cc_final: 0.8414 (tp) REVERT: C 218 ASP cc_start: 0.7888 (t70) cc_final: 0.7665 (t0) REVERT: C 256 ASP cc_start: 0.7673 (p0) cc_final: 0.7303 (p0) REVERT: C 408 MET cc_start: 0.9157 (tpp) cc_final: 0.8229 (tpp) REVERT: C 412 VAL cc_start: 0.9388 (t) cc_final: 0.9164 (m) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2443 time to fit residues: 120.4664 Evaluate side-chains 263 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 142 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 GLN ** C 472 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 = 0.3565 r_free = 0.3565 target = 0.132633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110627 restraints weight = 30772.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113659 restraints weight = 19001.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115788 restraints weight = 13493.060| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16294 Z= 0.186 Angle : 0.577 9.114 22106 Z= 0.282 Chirality : 0.043 0.181 2452 Planarity : 0.003 0.041 2970 Dihedral : 3.678 15.198 2208 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 2026 helix: 1.20 (0.20), residues: 746 sheet: -0.21 (0.27), residues: 398 loop : -0.88 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 487 HIS 0.002 0.001 HIS E 101 PHE 0.013 0.001 PHE A 230 TYR 0.025 0.002 TYR E 559 ARG 0.002 0.000 ARG E 497 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3085.03 seconds wall clock time: 56 minutes 29.52 seconds (3389.52 seconds total)