Starting phenix.real_space_refine on Sat May 18 00:34:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc8_28976/05_2024/8fc8_28976_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc8_28976/05_2024/8fc8_28976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc8_28976/05_2024/8fc8_28976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc8_28976/05_2024/8fc8_28976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc8_28976/05_2024/8fc8_28976_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc8_28976/05_2024/8fc8_28976_trim.pdb" } resolution = 3.47 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= 0.010 sd= 0.091 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: 6 Type Number sf(0) Gaussians S 112 5.16 5 Cl 8 4.86 5 C 12936 2.51 5 N 3236 2.21 5 O 3476 1.98 5 H 19384 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 39152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9711 Classifications: {'peptide': 617} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 9711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9711 Classifications: {'peptide': 617} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 9711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9711 Classifications: {'peptide': 617} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 9711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9711 Classifications: {'peptide': 617} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'XQ3': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'XQ3': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'XQ3': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'XQ3': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.19, per 1000 atoms: 0.41 Number of scatterers: 39152 At special positions: 0 Unit cell: (158.76, 158.76, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 112 16.00 O 3476 8.00 N 3236 7.00 C 12936 6.00 H 19384 1.00 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: 29.88 Conformation dependent library (CDL) restraints added in 4.3 seconds 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 68.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 222 through 228 removed outlier: 3.595A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.549A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.596A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.744A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.810A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.523A pdb=" N ALA A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.905A pdb=" N GLU A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.536A pdb=" N TYR A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.794A pdb=" N TYR A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 512 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 514 " --> pdb=" O ARG A 510 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 532 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.591A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.944A pdb=" N LEU A 551 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 removed outlier: 4.274A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.801A pdb=" N THR A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 636 removed outlier: 4.099A pdb=" N SER A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 679 removed outlier: 3.587A pdb=" N GLY A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 688 Processing helix chain 'A' and resid 691 through 709 Processing helix chain 'A' and resid 709 through 728 removed outlier: 4.507A pdb=" N ILE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 747 removed outlier: 3.559A pdb=" N SER A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.595A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.549A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.597A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 335 through 357 removed outlier: 3.744A pdb=" N LYS B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.811A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.522A pdb=" N ALA B 451 " --> pdb=" O HIS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.905A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 491 removed outlier: 3.537A pdb=" N TYR B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 535 removed outlier: 3.794A pdb=" N TYR B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 532 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.592A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 569 removed outlier: 3.944A pdb=" N LEU B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 588 removed outlier: 4.273A pdb=" N VAL B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.801A pdb=" N THR B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 636 removed outlier: 4.099A pdb=" N SER B 603 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 679 removed outlier: 3.587A pdb=" N GLY B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 691 through 709 Processing helix chain 'B' and resid 709 through 728 removed outlier: 4.507A pdb=" N ILE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 747 removed outlier: 3.559A pdb=" N SER B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 222 through 228 removed outlier: 3.595A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.549A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.596A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 335 through 357 removed outlier: 3.744A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.810A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 445 through 451 removed outlier: 3.524A pdb=" N ALA C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.905A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 491 removed outlier: 3.536A pdb=" N TYR C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 535 removed outlier: 3.794A pdb=" N TYR C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 512 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 513 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 514 " --> pdb=" O ARG C 510 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 532 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 544 removed outlier: 3.591A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 569 removed outlier: 3.944A pdb=" N LEU C 551 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 564 " --> pdb=" O VAL C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 removed outlier: 4.274A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 removed outlier: 3.800A pdb=" N THR C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 636 removed outlier: 4.099A pdb=" N SER C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 611 " --> pdb=" O GLN C 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 679 removed outlier: 3.587A pdb=" N GLY C 679 " --> pdb=" O LYS C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 688 Processing helix chain 'C' and resid 691 through 709 Processing helix chain 'C' and resid 709 through 728 removed outlier: 4.507A pdb=" N ILE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C 716 " --> pdb=" O ASN C 712 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C 717 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 747 removed outlier: 3.559A pdb=" N SER C 747 " --> pdb=" O ASP C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'D' and resid 151 through 161 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 222 through 228 removed outlier: 3.595A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.550A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.596A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 335 through 357 removed outlier: 3.744A pdb=" N LYS D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.811A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 445 through 451 removed outlier: 3.523A pdb=" N ALA D 451 " --> pdb=" O HIS D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.905A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 491 removed outlier: 3.537A pdb=" N TYR D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 535 removed outlier: 3.793A pdb=" N TYR D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 512 " --> pdb=" O TYR D 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 532 " --> pdb=" O ASN D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.592A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 569 removed outlier: 3.944A pdb=" N LEU D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 564 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 588 removed outlier: 4.273A pdb=" N VAL D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 595 removed outlier: 3.801A pdb=" N THR D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY D 595 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 636 removed outlier: 4.098A pdb=" N SER D 603 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE D 615 " --> pdb=" O PHE D 611 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 679 removed outlier: 3.587A pdb=" N GLY D 679 " --> pdb=" O LYS D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 688 Processing helix chain 'D' and resid 691 through 709 Processing helix chain 'D' and resid 709 through 728 removed outlier: 4.507A pdb=" N ILE D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D 716 " --> pdb=" O ASN D 712 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 747 removed outlier: 3.558A pdb=" N SER D 747 " --> pdb=" O ASP D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 411 removed outlier: 6.455A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 411 removed outlier: 6.455A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 411 removed outlier: 6.456A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 411 removed outlier: 6.454A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3195 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: 15.19 Time building geometry restraints manager: 30.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 19348 1.04 - 1.24: 2638 1.24 - 1.44: 6085 1.44 - 1.65: 11373 1.65 - 1.85: 196 Bond restraints: 39640 Sorted by residual: bond pdb=" C25 XQ3 B1001 " pdb=" N22 XQ3 B1001 " ideal model delta sigma weight residual 1.347 1.493 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C25 XQ3 D1001 " pdb=" N22 XQ3 D1001 " ideal model delta sigma weight residual 1.347 1.493 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C25 XQ3 A1001 " pdb=" N22 XQ3 A1001 " ideal model delta sigma weight residual 1.347 1.493 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C25 XQ3 C1002 " pdb=" N22 XQ3 C1002 " ideal model delta sigma weight residual 1.347 1.492 -0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C07 XQ3 D1001 " pdb=" N06 XQ3 D1001 " ideal model delta sigma weight residual 1.349 1.472 -0.123 2.00e-02 2.50e+03 3.75e+01 ... (remaining 39635 not shown) Histogram of bond angle deviations from ideal: 95.35 - 103.08: 145 103.08 - 110.82: 41590 110.82 - 118.56: 11560 118.56 - 126.29: 17782 126.29 - 134.03: 379 Bond angle restraints: 71456 Sorted by residual: angle pdb=" O31 XQ3 C1002 " pdb=" S30 XQ3 C1002 " pdb=" O40 XQ3 C1002 " ideal model delta sigma weight residual 119.28 102.14 17.14 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O31 XQ3 D1001 " pdb=" S30 XQ3 D1001 " pdb=" O40 XQ3 D1001 " ideal model delta sigma weight residual 119.28 102.16 17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O31 XQ3 A1001 " pdb=" S30 XQ3 A1001 " pdb=" O40 XQ3 A1001 " ideal model delta sigma weight residual 119.28 102.16 17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O31 XQ3 B1001 " pdb=" S30 XQ3 B1001 " pdb=" O40 XQ3 B1001 " ideal model delta sigma weight residual 119.28 102.17 17.11 3.00e+00 1.11e-01 3.25e+01 angle pdb=" CAT Y01 D1002 " pdb=" CBH Y01 D1002 " pdb=" CBF Y01 D1002 " ideal model delta sigma weight residual 108.46 95.35 13.11 3.00e+00 1.11e-01 1.91e+01 ... (remaining 71451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 17674 16.66 - 33.31: 882 33.31 - 49.97: 275 49.97 - 66.62: 161 66.62 - 83.28: 12 Dihedral angle restraints: 19004 sinusoidal: 10212 harmonic: 8792 Sorted by residual: dihedral pdb=" CA MET A 713 " pdb=" C MET A 713 " pdb=" N LEU A 714 " pdb=" CA LEU A 714 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA MET D 713 " pdb=" C MET D 713 " pdb=" N LEU D 714 " pdb=" CA LEU D 714 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.49e+00 dihedral pdb=" CA CYS B 353 " pdb=" CB CYS B 353 " pdb=" SG CYS B 353 " pdb=" HG CYS B 353 " ideal model delta sinusoidal sigma weight residual 60.00 119.09 -59.09 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 19001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3035 0.084 - 0.167: 105 0.167 - 0.251: 8 0.251 - 0.335: 4 0.335 - 0.419: 12 Chirality restraints: 3164 Sorted by residual: chirality pdb=" CBH Y01 D1002 " pdb=" CAT Y01 D1002 " pdb=" CAZ Y01 D1002 " pdb=" CBF Y01 D1002 " both_signs ideal model delta sigma weight residual False -2.85 -3.27 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CBH Y01 C1003 " pdb=" CAT Y01 C1003 " pdb=" CAZ Y01 C1003 " pdb=" CBF Y01 C1003 " both_signs ideal model delta sigma weight residual False -2.85 -3.27 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CBH Y01 C1001 " pdb=" CAT Y01 C1001 " pdb=" CAZ Y01 C1001 " pdb=" CBF Y01 C1001 " both_signs ideal model delta sigma weight residual False -2.85 -3.27 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 3161 not shown) Planarity restraints: 5776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 528 " -0.094 2.00e-02 2.50e+03 8.90e-02 1.19e+02 pdb=" CG ASN B 528 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 528 " 0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN B 528 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 528 " -0.128 2.00e-02 2.50e+03 pdb="HD22 ASN B 528 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 528 " 0.094 2.00e-02 2.50e+03 8.89e-02 1.19e+02 pdb=" CG ASN C 528 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN C 528 " -0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN C 528 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 528 " 0.128 2.00e-02 2.50e+03 pdb="HD22 ASN C 528 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 528 " 0.094 2.00e-02 2.50e+03 8.88e-02 1.18e+02 pdb=" CG ASN A 528 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 528 " -0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN A 528 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 528 " 0.128 2.00e-02 2.50e+03 pdb="HD22 ASN A 528 " -0.122 2.00e-02 2.50e+03 ... (remaining 5773 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4298 2.26 - 2.84: 88444 2.84 - 3.43: 97836 3.43 - 4.01: 129223 4.01 - 4.60: 202683 Nonbonded interactions: 522484 Sorted by model distance: nonbonded pdb=" HH TYR D 346 " pdb=" OE2 GLU D 363 " model vdw 1.671 1.850 nonbonded pdb=" HH TYR C 346 " pdb=" OE2 GLU C 363 " model vdw 1.671 1.850 nonbonded pdb=" HH TYR A 346 " pdb=" OE2 GLU A 363 " model vdw 1.672 1.850 nonbonded pdb=" HH TYR B 346 " pdb=" OE2 GLU B 363 " model vdw 1.672 1.850 nonbonded pdb=" OE1 GLU D 495 " pdb=" H GLU D 495 " model vdw 1.682 1.850 ... (remaining 522479 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 150 through 788) selection = (chain 'B' and resid 150 through 788) selection = (chain 'C' and resid 150 through 788) selection = (chain 'D' and resid 150 through 788) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.680 Extract box with map and model: 5.740 Check model and map are aligned: 0.270 Set scattering table: 0.390 Process input model: 115.660 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.006 0.146 20256 Z= 0.348 Angle : 0.676 17.139 27556 Z= 0.297 Chirality : 0.044 0.419 3164 Planarity : 0.003 0.038 3408 Dihedral : 11.822 83.280 7544 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.19 % Allowed : 5.44 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2452 helix: 1.85 (0.14), residues: 1508 sheet: -2.12 (0.61), residues: 76 loop : -0.78 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 733 HIS 0.003 0.001 HIS B 243 PHE 0.011 0.001 PHE B 341 TYR 0.008 0.001 TYR D 419 ARG 0.002 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 543 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 539 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 267 GLN cc_start: 0.8159 (mt0) cc_final: 0.7879 (mt0) REVERT: A 605 MET cc_start: 0.7871 (ptt) cc_final: 0.7631 (ptt) REVERT: A 734 LYS cc_start: 0.8172 (tttp) cc_final: 0.7846 (ptmm) REVERT: A 737 TRP cc_start: 0.7769 (t60) cc_final: 0.7405 (t60) REVERT: B 256 LEU cc_start: 0.8894 (tp) cc_final: 0.8661 (mp) REVERT: B 682 ASP cc_start: 0.6590 (t0) cc_final: 0.6383 (p0) REVERT: B 683 LEU cc_start: 0.8455 (mt) cc_final: 0.7940 (mp) REVERT: B 734 LYS cc_start: 0.8074 (tttp) cc_final: 0.7670 (ptmm) REVERT: C 295 THR cc_start: 0.6364 (p) cc_final: 0.5978 (p) REVERT: C 587 MET cc_start: 0.7401 (ttp) cc_final: 0.7142 (ttp) REVERT: C 605 MET cc_start: 0.7746 (ptt) cc_final: 0.7518 (ptt) REVERT: C 682 ASP cc_start: 0.6342 (t0) cc_final: 0.6007 (p0) REVERT: C 734 LYS cc_start: 0.7800 (tttp) cc_final: 0.7185 (ptmm) REVERT: D 244 ILE cc_start: 0.7946 (mt) cc_final: 0.7679 (mt) REVERT: D 256 LEU cc_start: 0.8907 (tp) cc_final: 0.8703 (mp) REVERT: D 365 VAL cc_start: 0.8303 (t) cc_final: 0.8045 (m) REVERT: D 582 LEU cc_start: 0.8261 (tp) cc_final: 0.7863 (tp) REVERT: D 605 MET cc_start: 0.7729 (ptt) cc_final: 0.7445 (ptt) REVERT: D 707 PHE cc_start: 0.6733 (t80) cc_final: 0.6509 (t80) REVERT: D 734 LYS cc_start: 0.8246 (tttp) cc_final: 0.7722 (ptmm) outliers start: 4 outliers final: 3 residues processed: 543 average time/residue: 0.7487 time to fit residues: 626.7742 Evaluate side-chains 324 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 321 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain D residue 341 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 1.9990 chunk 184 optimal weight: 30.0000 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 787 HIS C 550 GLN D 297 GLN D 712 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20256 Z= 0.204 Angle : 0.530 5.762 27556 Z= 0.282 Chirality : 0.035 0.141 3164 Planarity : 0.004 0.042 3408 Dihedral : 6.640 56.751 3154 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.70 % Allowed : 12.38 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2452 helix: 1.71 (0.13), residues: 1528 sheet: -2.06 (0.59), residues: 76 loop : -0.73 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 733 HIS 0.005 0.001 HIS C 326 PHE 0.028 0.002 PHE B 751 TYR 0.014 0.001 TYR B 502 ARG 0.008 0.000 ARG D 746 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 386 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 351 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 201 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7959 (p0) REVERT: A 682 ASP cc_start: 0.6667 (t0) cc_final: 0.5937 (m-30) REVERT: A 713 MET cc_start: 0.7737 (tmm) cc_final: 0.7434 (tmm) REVERT: A 737 TRP cc_start: 0.7775 (t60) cc_final: 0.7547 (t60) REVERT: A 743 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8508 (m-30) REVERT: B 333 ASP cc_start: 0.7379 (t0) cc_final: 0.7075 (m-30) REVERT: B 605 MET cc_start: 0.7977 (ptt) cc_final: 0.7705 (ptt) REVERT: B 682 ASP cc_start: 0.6582 (t0) cc_final: 0.5885 (p0) REVERT: B 683 LEU cc_start: 0.8598 (mt) cc_final: 0.7958 (mp) REVERT: C 201 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8060 (p0) REVERT: C 365 VAL cc_start: 0.8330 (t) cc_final: 0.7985 (m) REVERT: C 482 MET cc_start: 0.7166 (mmt) cc_final: 0.6757 (mmp) REVERT: C 578 MET cc_start: 0.7909 (ttp) cc_final: 0.7296 (ttm) REVERT: C 682 ASP cc_start: 0.6438 (t0) cc_final: 0.5634 (p0) REVERT: D 244 ILE cc_start: 0.8021 (mt) cc_final: 0.7746 (mt) REVERT: D 256 LEU cc_start: 0.8966 (tp) cc_final: 0.8688 (mp) REVERT: D 333 ASP cc_start: 0.7404 (t0) cc_final: 0.7054 (m-30) REVERT: D 365 VAL cc_start: 0.8267 (t) cc_final: 0.7947 (m) REVERT: D 396 ASP cc_start: 0.7588 (t0) cc_final: 0.7366 (t0) REVERT: D 582 LEU cc_start: 0.8307 (tp) cc_final: 0.7927 (tp) REVERT: D 676 LEU cc_start: 0.8089 (tp) cc_final: 0.7837 (tp) REVERT: D 682 ASP cc_start: 0.6535 (t0) cc_final: 0.5910 (p0) REVERT: D 707 PHE cc_start: 0.6758 (t80) cc_final: 0.6477 (t80) outliers start: 35 outliers final: 19 residues processed: 380 average time/residue: 0.6889 time to fit residues: 404.9710 Evaluate side-chains 337 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 315 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 630 SER Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 743 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 0.0040 chunk 239 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN B 492 GLN C 440 ASN C 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20256 Z= 0.162 Angle : 0.488 5.570 27556 Z= 0.256 Chirality : 0.034 0.132 3164 Planarity : 0.004 0.042 3408 Dihedral : 6.154 51.802 3154 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.70 % Allowed : 12.62 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2452 helix: 1.84 (0.13), residues: 1544 sheet: -2.06 (0.58), residues: 76 loop : -0.65 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 733 HIS 0.003 0.001 HIS C 326 PHE 0.016 0.001 PHE C 751 TYR 0.012 0.001 TYR A 303 ARG 0.003 0.000 ARG D 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 336 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 201 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7900 (p0) REVERT: A 682 ASP cc_start: 0.6611 (t0) cc_final: 0.6081 (p0) REVERT: A 707 PHE cc_start: 0.6881 (t80) cc_final: 0.6471 (t80) REVERT: A 713 MET cc_start: 0.7826 (tmm) cc_final: 0.7478 (tmm) REVERT: A 737 TRP cc_start: 0.7687 (t60) cc_final: 0.7482 (t60) REVERT: B 333 ASP cc_start: 0.7337 (t0) cc_final: 0.7055 (m-30) REVERT: B 365 VAL cc_start: 0.8264 (t) cc_final: 0.7918 (m) REVERT: B 482 MET cc_start: 0.7258 (mmp) cc_final: 0.6705 (mmp) REVERT: C 201 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8099 (p0) REVERT: C 365 VAL cc_start: 0.8311 (t) cc_final: 0.7962 (m) REVERT: C 482 MET cc_start: 0.7078 (mmt) cc_final: 0.6742 (mmp) REVERT: C 578 MET cc_start: 0.7934 (ttp) cc_final: 0.7332 (ttm) REVERT: C 622 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5426 (mt) REVERT: D 333 ASP cc_start: 0.7494 (t0) cc_final: 0.7171 (m-30) REVERT: D 365 VAL cc_start: 0.8257 (t) cc_final: 0.7917 (m) REVERT: D 396 ASP cc_start: 0.7810 (t0) cc_final: 0.7539 (t0) REVERT: D 582 LEU cc_start: 0.8309 (tp) cc_final: 0.8015 (tp) REVERT: D 707 PHE cc_start: 0.6891 (t80) cc_final: 0.6487 (t80) outliers start: 35 outliers final: 23 residues processed: 361 average time/residue: 0.6446 time to fit residues: 371.4540 Evaluate side-chains 351 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 325 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 630 SER Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 743 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.0070 chunk 166 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20256 Z= 0.151 Angle : 0.466 5.704 27556 Z= 0.244 Chirality : 0.033 0.157 3164 Planarity : 0.004 0.043 3408 Dihedral : 5.832 49.337 3154 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.75 % Allowed : 13.25 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.17), residues: 2452 helix: 1.90 (0.13), residues: 1536 sheet: -1.86 (0.59), residues: 76 loop : -0.58 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 733 HIS 0.005 0.000 HIS D 252 PHE 0.016 0.001 PHE C 751 TYR 0.011 0.001 TYR B 502 ARG 0.006 0.000 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 374 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 338 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 201 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7818 (p0) REVERT: A 682 ASP cc_start: 0.6662 (t0) cc_final: 0.6119 (p0) REVERT: A 713 MET cc_start: 0.7835 (tmm) cc_final: 0.7455 (tmm) REVERT: B 365 VAL cc_start: 0.8267 (t) cc_final: 0.7908 (m) REVERT: B 482 MET cc_start: 0.7232 (mmp) cc_final: 0.6714 (mmp) REVERT: B 578 MET cc_start: 0.7996 (ttp) cc_final: 0.7454 (ttm) REVERT: B 707 PHE cc_start: 0.6781 (t80) cc_final: 0.6304 (t80) REVERT: C 201 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8109 (p0) REVERT: C 365 VAL cc_start: 0.8298 (t) cc_final: 0.7952 (m) REVERT: C 482 MET cc_start: 0.7109 (mmt) cc_final: 0.6808 (mmp) REVERT: C 578 MET cc_start: 0.7979 (ttp) cc_final: 0.7407 (ttm) REVERT: C 622 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5301 (mt) REVERT: D 215 ASP cc_start: 0.8496 (m-30) cc_final: 0.8221 (m-30) REVERT: D 365 VAL cc_start: 0.8248 (t) cc_final: 0.7907 (m) REVERT: D 396 ASP cc_start: 0.7922 (t0) cc_final: 0.7637 (t0) REVERT: D 582 LEU cc_start: 0.8383 (tp) cc_final: 0.8139 (tp) REVERT: D 676 LEU cc_start: 0.8197 (tp) cc_final: 0.7872 (tp) REVERT: D 707 PHE cc_start: 0.6895 (t80) cc_final: 0.6420 (t80) outliers start: 36 outliers final: 19 residues processed: 370 average time/residue: 0.6150 time to fit residues: 368.8749 Evaluate side-chains 342 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 320 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 630 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 743 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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: 0.7130 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20256 Z= 0.191 Angle : 0.478 6.517 27556 Z= 0.252 Chirality : 0.034 0.125 3164 Planarity : 0.004 0.047 3408 Dihedral : 5.750 49.580 3154 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.94 % Allowed : 13.83 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2452 helix: 1.90 (0.13), residues: 1540 sheet: -1.94 (0.58), residues: 76 loop : -0.59 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 733 HIS 0.009 0.001 HIS D 252 PHE 0.012 0.001 PHE A 185 TYR 0.011 0.001 TYR D 556 ARG 0.005 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 333 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 201 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7767 (p0) REVERT: A 682 ASP cc_start: 0.6763 (t0) cc_final: 0.6108 (p0) REVERT: A 683 LEU cc_start: 0.8662 (mt) cc_final: 0.8256 (mt) REVERT: A 713 MET cc_start: 0.7859 (tmm) cc_final: 0.7457 (tmm) REVERT: B 215 ASP cc_start: 0.8509 (m-30) cc_final: 0.8252 (m-30) REVERT: B 365 VAL cc_start: 0.8326 (t) cc_final: 0.7985 (m) REVERT: B 578 MET cc_start: 0.8022 (ttp) cc_final: 0.7483 (ttm) REVERT: B 707 PHE cc_start: 0.6674 (t80) cc_final: 0.6457 (t80) REVERT: B 713 MET cc_start: 0.7739 (tmm) cc_final: 0.7113 (ttp) REVERT: C 365 VAL cc_start: 0.8352 (t) cc_final: 0.8031 (m) REVERT: C 482 MET cc_start: 0.7074 (mmt) cc_final: 0.6764 (mmp) REVERT: C 578 MET cc_start: 0.7957 (ttp) cc_final: 0.7428 (ttm) REVERT: C 622 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5325 (mt) REVERT: C 628 TYR cc_start: 0.8162 (m-80) cc_final: 0.7809 (m-80) REVERT: D 215 ASP cc_start: 0.8481 (m-30) cc_final: 0.8213 (m-30) REVERT: D 365 VAL cc_start: 0.8330 (t) cc_final: 0.7997 (m) REVERT: D 396 ASP cc_start: 0.7953 (t0) cc_final: 0.7679 (t0) REVERT: D 582 LEU cc_start: 0.8463 (tp) cc_final: 0.8218 (tp) REVERT: D 707 PHE cc_start: 0.6944 (t80) cc_final: 0.6434 (t80) outliers start: 40 outliers final: 24 residues processed: 363 average time/residue: 0.6231 time to fit residues: 365.8101 Evaluate side-chains 343 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 317 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 630 SER Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 634 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 30.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.7168 moved from start: 0.4226 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: