Starting phenix.real_space_refine on Fri Jun 20 11:04:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uza_20954/06_2025/6uza_20954.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uza_20954/06_2025/6uza_20954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uza_20954/06_2025/6uza_20954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uza_20954/06_2025/6uza_20954.map" model { file = "/net/cci-nas-00/data/ceres_data/6uza_20954/06_2025/6uza_20954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uza_20954/06_2025/6uza_20954.cif" } resolution = 3.08 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 140 5.16 5 C 15296 2.51 5 N 3808 2.21 5 O 4032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23284 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5659 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 24, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 187 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 203 Unusual residues: {'R0G': 1, 'S9Y': 1, 'SBJ': 2, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'R0G': 1, 'S9Y': 1, 'SBJ': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'R0G': 1, 'S9Y': 1, 'SBJ': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 121 Unusual residues: {'R0G': 1, 'S9Y': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 15.51, per 1000 atoms: 0.67 Number of scatterers: 23284 At special positions: 0 Unit cell: (128.96, 128.96, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 8 15.00 O 4032 8.00 N 3808 7.00 C 15296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 258 " distance=2.04 Simple disulfide: pdb=" SG CYS C 255 " - pdb=" SG CYS C 258 " distance=2.04 Simple disulfide: pdb=" SG CYS D 255 " - pdb=" SG CYS D 258 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 5.52 Conformation dependent library (CDL) restraints added in 2.8 seconds 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5608 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 65.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.614A pdb=" N GLN A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.862A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 3.862A pdb=" N ASN A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.846A pdb=" N LYS A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.767A pdb=" N ILE A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.621A pdb=" N VAL A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 392 removed outlier: 4.141A pdb=" N GLN A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.619A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 461 removed outlier: 3.699A pdb=" N PHE A 450 " --> pdb=" O HIS A 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 517 removed outlier: 3.669A pdb=" N GLU A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 556 removed outlier: 3.940A pdb=" N MET A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 removed outlier: 3.731A pdb=" N TRP A 586 " --> pdb=" O ARG A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 606 removed outlier: 3.542A pdb=" N GLY A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.877A pdb=" N ILE A 610 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 611 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU A 614 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Proline residue: A 615 - end of helix Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 637 through 654 Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.536A pdb=" N LEU A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.680A pdb=" N SER A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 691 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 692 " --> pdb=" O LYS A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 687 through 692' Processing helix chain 'A' and resid 697 through 729 removed outlier: 3.523A pdb=" N GLU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 751 removed outlier: 3.609A pdb=" N VAL A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 Processing helix chain 'A' and resid 880 through 918 removed outlier: 3.969A pdb=" N LEU A 884 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 257 through 265 removed outlier: 3.614A pdb=" N GLN B 262 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.862A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 removed outlier: 3.862A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 334 removed outlier: 3.846A pdb=" N LYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 329 " --> pdb=" O CYS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.767A pdb=" N ILE B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.621A pdb=" N VAL B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 392 removed outlier: 4.141A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 390 " --> pdb=" O GLN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.619A pdb=" N LEU B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 461 removed outlier: 3.699A pdb=" N PHE B 450 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 517 removed outlier: 3.669A pdb=" N GLU B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 556 removed outlier: 3.940A pdb=" N MET B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.731A pdb=" N TRP B 586 " --> pdb=" O ARG B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 606 removed outlier: 3.542A pdb=" N GLY B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 removed outlier: 3.877A pdb=" N ILE B 610 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 611 " --> pdb=" O SER B 608 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU B 614 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Proline residue: B 615 - end of helix Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 637 through 654 Processing helix chain 'B' and resid 670 through 680 removed outlier: 3.536A pdb=" N LEU B 678 " --> pdb=" O SER B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 removed outlier: 3.680A pdb=" N SER B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 691 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 692 " --> pdb=" O LYS B 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 687 through 692' Processing helix chain 'B' and resid 697 through 729 removed outlier: 3.523A pdb=" N GLU B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 751 removed outlier: 3.609A pdb=" N VAL B 740 " --> pdb=" O ASP B 736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP B 742 " --> pdb=" O ALA B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 875 Processing helix chain 'B' and resid 880 through 918 removed outlier: 3.969A pdb=" N LEU B 884 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 885 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B 886 " --> pdb=" O GLY B 882 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 887 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 916 " --> pdb=" O LEU B 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 135 through 141 Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.614A pdb=" N GLN C 262 " --> pdb=" O CYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.862A pdb=" N LEU C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 removed outlier: 3.862A pdb=" N ASN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 removed outlier: 3.846A pdb=" N LYS C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 329 " --> pdb=" O CYS C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.767A pdb=" N ILE C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.621A pdb=" N VAL C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 392 removed outlier: 4.141A pdb=" N GLN C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.619A pdb=" N LEU C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 461 removed outlier: 3.699A pdb=" N PHE C 450 " --> pdb=" O HIS C 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 517 removed outlier: 3.669A pdb=" N GLU C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 556 removed outlier: 3.940A pdb=" N MET C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 534 " --> pdb=" O ASP C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 removed outlier: 3.731A pdb=" N TRP C 586 " --> pdb=" O ARG C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 606 removed outlier: 3.542A pdb=" N GLY C 597 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE C 601 " --> pdb=" O GLY C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 617 removed outlier: 3.877A pdb=" N ILE C 610 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 611 " --> pdb=" O SER C 608 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU C 614 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 620 through 629 Processing helix chain 'C' and resid 637 through 654 Processing helix chain 'C' and resid 670 through 680 removed outlier: 3.536A pdb=" N LEU C 678 " --> pdb=" O SER C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 692 removed outlier: 3.680A pdb=" N SER C 690 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 691 " --> pdb=" O VAL C 688 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 692 " --> pdb=" O LYS C 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 687 through 692' Processing helix chain 'C' and resid 697 through 729 removed outlier: 3.523A pdb=" N GLU C 701 " --> pdb=" O HIS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 751 removed outlier: 3.609A pdb=" N VAL C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 875 Processing helix chain 'C' and resid 880 through 918 removed outlier: 3.969A pdb=" N LEU C 884 " --> pdb=" O ASN C 880 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 885 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 886 " --> pdb=" O GLY C 882 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 257 through 265 removed outlier: 3.614A pdb=" N GLN D 262 " --> pdb=" O CYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.862A pdb=" N LEU D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 311 removed outlier: 3.862A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 removed outlier: 3.846A pdb=" N LYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 329 " --> pdb=" O CYS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 347 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.767A pdb=" N ILE D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.621A pdb=" N VAL D 378 " --> pdb=" O VAL D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 392 removed outlier: 4.141A pdb=" N GLN D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER D 389 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 390 " --> pdb=" O GLN D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.619A pdb=" N LEU D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 461 removed outlier: 3.699A pdb=" N PHE D 450 " --> pdb=" O HIS D 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 517 removed outlier: 3.669A pdb=" N GLU D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 556 removed outlier: 3.940A pdb=" N MET D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 534 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 586 removed outlier: 3.731A pdb=" N TRP D 586 " --> pdb=" O ARG D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 606 removed outlier: 3.542A pdb=" N GLY D 597 " --> pdb=" O ILE D 593 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 617 removed outlier: 3.877A pdb=" N ILE D 610 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 611 " --> pdb=" O SER D 608 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU D 614 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Proline residue: D 615 - end of helix Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 637 through 654 Processing helix chain 'D' and resid 670 through 680 removed outlier: 3.536A pdb=" N LEU D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 removed outlier: 3.680A pdb=" N SER D 690 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 691 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 692 " --> pdb=" O LYS D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 687 through 692' Processing helix chain 'D' and resid 697 through 729 removed outlier: 3.523A pdb=" N GLU D 701 " --> pdb=" O HIS D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 751 removed outlier: 3.609A pdb=" N VAL D 740 " --> pdb=" O ASP D 736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP D 742 " --> pdb=" O ALA D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 875 Processing helix chain 'D' and resid 880 through 918 removed outlier: 3.969A pdb=" N LEU D 884 " --> pdb=" O ASN D 880 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS D 885 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU D 886 " --> pdb=" O GLY D 882 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 887 " --> pdb=" O GLU D 883 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 916 " --> pdb=" O LEU D 912 " (cutoff:3.500A) 1240 hydrogen bonds defined for protein. 3660 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: 6.35 Time building geometry restraints manager: 6.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3600 1.30 - 1.43: 6440 1.43 - 1.56: 13436 1.56 - 1.69: 88 1.69 - 1.83: 248 Bond restraints: 23812 Sorted by residual: bond pdb=" O5 S9Y C1003 " pdb=" P S9Y C1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y A1002 " pdb=" P S9Y A1002 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y B1003 " pdb=" P S9Y B1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y D1003 " pdb=" P S9Y D1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C21 R0G B1002 " pdb=" C22 R0G B1002 " ideal model delta sigma weight residual 1.423 1.556 -0.133 2.00e-02 2.50e+03 4.44e+01 ... (remaining 23807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 31835 3.66 - 7.32: 365 7.32 - 10.98: 76 10.98 - 14.64: 4 14.64 - 18.30: 12 Bond angle restraints: 32292 Sorted by residual: angle pdb=" N VAL A 576 " pdb=" CA VAL A 576 " pdb=" C VAL A 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL B 576 " pdb=" CA VAL B 576 " pdb=" C VAL B 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL D 576 " pdb=" CA VAL D 576 " pdb=" C VAL D 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL C 576 " pdb=" CA VAL C 576 " pdb=" C VAL C 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" O3P S9Y A1002 " pdb=" P S9Y A1002 " pdb=" O5 S9Y A1002 " ideal model delta sigma weight residual 94.12 112.42 -18.30 3.00e+00 1.11e-01 3.72e+01 ... (remaining 32287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 14064 30.12 - 60.24: 536 60.24 - 90.36: 28 90.36 - 120.48: 0 120.48 - 150.60: 4 Dihedral angle restraints: 14632 sinusoidal: 5984 harmonic: 8648 Sorted by residual: dihedral pdb=" CA ASN B 256 " pdb=" C ASN B 256 " pdb=" N ASP B 257 " pdb=" CA ASP B 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASN A 256 " pdb=" C ASN A 256 " pdb=" N ASP A 257 " pdb=" CA ASP A 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASN C 256 " pdb=" C ASN C 256 " pdb=" N ASP C 257 " pdb=" CA ASP C 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 14629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3448 0.103 - 0.206: 184 0.206 - 0.309: 36 0.309 - 0.412: 8 0.412 - 0.515: 8 Chirality restraints: 3684 Sorted by residual: chirality pdb=" C2 SBJ A1003 " pdb=" C1 SBJ A1003 " pdb=" C3 SBJ A1003 " pdb=" O2 SBJ A1003 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" C2 SBJ B1004 " pdb=" C1 SBJ B1004 " pdb=" C3 SBJ B1004 " pdb=" O2 SBJ B1004 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" C2 SBJ C1004 " pdb=" C1 SBJ C1004 " pdb=" C3 SBJ C1004 " pdb=" O2 SBJ C1004 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 ... (remaining 3681 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 758 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C ARG C 758 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG C 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR C 759 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 758 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C ARG A 758 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG A 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR A 759 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 758 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C ARG B 758 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG B 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR B 759 " -0.016 2.00e-02 2.50e+03 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7748 2.85 - 3.36: 20216 3.36 - 3.88: 36295 3.88 - 4.39: 43364 4.39 - 4.90: 75205 Nonbonded interactions: 182828 Sorted by model distance: nonbonded pdb=" O SER B 589 " pdb=" OG SER B 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER A 589 " pdb=" OG SER A 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER C 589 " pdb=" OG SER C 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER D 589 " pdb=" OG SER D 589 " model vdw 2.338 3.040 nonbonded pdb=" O PRO B 283 " pdb=" OG SER B 287 " model vdw 2.338 3.040 ... (remaining 182823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 85 through 920) selection = (chain 'B' and resid 85 through 920) selection = (chain 'C' and resid 85 through 920) selection = (chain 'D' and resid 85 through 920) } 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 50.450 Find NCS groups from input model: 1.220 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: 59.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.151 23816 Z= 0.408 Angle : 1.054 18.304 32300 Z= 0.528 Chirality : 0.062 0.515 3684 Planarity : 0.007 0.068 3956 Dihedral : 15.174 150.597 9012 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -3.92 (0.12), residues: 2904 helix: -2.47 (0.09), residues: 1920 sheet: None (None), residues: 0 loop : -2.49 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 514 HIS 0.003 0.001 HIS C 183 PHE 0.020 0.002 PHE C 537 TYR 0.020 0.002 TYR D 209 ARG 0.005 0.001 ARG A 758 Details of bonding type rmsd hydrogen bonds : bond 0.13583 ( 1240) hydrogen bonds : angle 5.37542 ( 3660) SS BOND : bond 0.00737 ( 4) SS BOND : angle 2.39416 ( 8) covalent geometry : bond 0.00831 (23812) covalent geometry : angle 1.05374 (32292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 2.411 Fit side-chains REVERT: A 441 MET cc_start: 0.7995 (mmm) cc_final: 0.7746 (mmp) REVERT: A 689 LYS cc_start: 0.8440 (ptmt) cc_final: 0.8178 (ptmt) REVERT: A 696 ASN cc_start: 0.8072 (t0) cc_final: 0.7871 (t0) REVERT: A 881 GLU cc_start: 0.8157 (tt0) cc_final: 0.7757 (mt-10) REVERT: B 441 MET cc_start: 0.7997 (mmm) cc_final: 0.7751 (mmp) REVERT: B 689 LYS cc_start: 0.8445 (ptmt) cc_final: 0.8183 (ptmt) REVERT: B 696 ASN cc_start: 0.8077 (t0) cc_final: 0.7875 (t0) REVERT: B 881 GLU cc_start: 0.8166 (tt0) cc_final: 0.7764 (mt-10) REVERT: C 441 MET cc_start: 0.7995 (mmm) cc_final: 0.7748 (mmp) REVERT: C 689 LYS cc_start: 0.8442 (ptmt) cc_final: 0.8180 (ptmt) REVERT: C 696 ASN cc_start: 0.8076 (t0) cc_final: 0.7872 (t0) REVERT: C 881 GLU cc_start: 0.8166 (tt0) cc_final: 0.7764 (mt-10) REVERT: D 441 MET cc_start: 0.7993 (mmm) cc_final: 0.7742 (mmp) REVERT: D 689 LYS cc_start: 0.8443 (ptmt) cc_final: 0.8178 (ptmt) REVERT: D 696 ASN cc_start: 0.8076 (t0) cc_final: 0.7873 (t0) REVERT: D 881 GLU cc_start: 0.8160 (tt0) cc_final: 0.7759 (mt-10) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.3866 time to fit residues: 208.9859 Evaluate side-chains 288 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 265 optimal weight: 0.0570 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 358 HIS A 380 HIS A 384 GLN A 446 HIS A 550 HIS A 728 ASN B 157 ASN B 358 HIS B 380 HIS B 384 GLN B 446 HIS B 550 HIS B 728 ASN C 157 ASN C 358 HIS C 380 HIS C 384 GLN C 446 HIS C 550 HIS C 728 ASN D 157 ASN D 358 HIS D 380 HIS D 384 GLN D 446 HIS D 550 HIS D 728 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121383 restraints weight = 25103.836| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.10 r_work: 0.3284 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23816 Z= 0.120 Angle : 0.493 6.265 32300 Z= 0.262 Chirality : 0.038 0.122 3684 Planarity : 0.004 0.045 3956 Dihedral : 9.138 98.173 4076 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.71 % Allowed : 9.22 % Favored : 90.07 % 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: -1.59 (0.15), residues: 2904 helix: -0.50 (0.11), residues: 1940 sheet: None (None), residues: 0 loop : -2.05 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 514 HIS 0.002 0.001 HIS C 183 PHE 0.009 0.001 PHE B 548 TYR 0.009 0.001 TYR A 209 ARG 0.002 0.000 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 1240) hydrogen bonds : angle 3.41109 ( 3660) SS BOND : bond 0.01065 ( 4) SS BOND : angle 3.54008 ( 8) covalent geometry : bond 0.00289 (23812) covalent geometry : angle 0.48961 (32292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 328 time to evaluate : 4.826 Fit side-chains REVERT: A 116 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7606 (ttpt) REVERT: A 262 GLN cc_start: 0.7912 (tt0) cc_final: 0.7474 (mt0) REVERT: A 441 MET cc_start: 0.8361 (mmm) cc_final: 0.8077 (mmp) REVERT: A 689 LYS cc_start: 0.8615 (ptmt) cc_final: 0.8313 (ptmt) REVERT: A 696 ASN cc_start: 0.8173 (t0) cc_final: 0.7844 (t0) REVERT: A 881 GLU cc_start: 0.8763 (tt0) cc_final: 0.8182 (mt-10) REVERT: B 116 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7596 (ttpt) REVERT: B 262 GLN cc_start: 0.7929 (tt0) cc_final: 0.7487 (mt0) REVERT: B 441 MET cc_start: 0.8368 (mmm) cc_final: 0.8088 (mmp) REVERT: B 689 LYS cc_start: 0.8615 (ptmt) cc_final: 0.8310 (ptmt) REVERT: B 696 ASN cc_start: 0.8150 (t0) cc_final: 0.7821 (t0) REVERT: B 881 GLU cc_start: 0.8766 (tt0) cc_final: 0.8186 (mt-10) REVERT: C 116 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7586 (ttpt) REVERT: C 262 GLN cc_start: 0.7927 (tt0) cc_final: 0.7488 (mt0) REVERT: C 441 MET cc_start: 0.8363 (mmm) cc_final: 0.8080 (mmp) REVERT: C 689 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8300 (ptmt) REVERT: C 696 ASN cc_start: 0.8166 (t0) cc_final: 0.7838 (t0) REVERT: C 881 GLU cc_start: 0.8770 (tt0) cc_final: 0.8189 (mt-10) REVERT: D 116 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7598 (ttpt) REVERT: D 262 GLN cc_start: 0.7919 (tt0) cc_final: 0.7481 (mt0) REVERT: D 441 MET cc_start: 0.8357 (mmm) cc_final: 0.8076 (mmp) REVERT: D 689 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8312 (ptmt) REVERT: D 696 ASN cc_start: 0.8168 (t0) cc_final: 0.7839 (t0) REVERT: D 881 GLU cc_start: 0.8769 (tt0) cc_final: 0.8189 (mt-10) outliers start: 16 outliers final: 12 residues processed: 336 average time/residue: 0.3759 time to fit residues: 195.1399 Evaluate side-chains 320 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 308 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 183 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 193 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122749 restraints weight = 24864.754| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.09 r_work: 0.3298 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23816 Z= 0.102 Angle : 0.453 5.975 32300 Z= 0.242 Chirality : 0.037 0.135 3684 Planarity : 0.004 0.036 3956 Dihedral : 8.209 74.145 4076 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.91 % Allowed : 9.44 % Favored : 88.65 % 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: -0.44 (0.16), residues: 2904 helix: 0.49 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : -1.80 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 514 HIS 0.002 0.000 HIS C 183 PHE 0.016 0.001 PHE C 407 TYR 0.008 0.001 TYR D 209 ARG 0.002 0.000 ARG B 629 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1240) hydrogen bonds : angle 3.03706 ( 3660) SS BOND : bond 0.01044 ( 4) SS BOND : angle 3.36549 ( 8) covalent geometry : bond 0.00243 (23812) covalent geometry : angle 0.45013 (32292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 2.636 Fit side-chains REVERT: A 262 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: A 339 THR cc_start: 0.8716 (t) cc_final: 0.8433 (m) REVERT: A 441 MET cc_start: 0.8312 (mmm) cc_final: 0.8030 (mmp) REVERT: A 507 TRP cc_start: 0.8443 (t-100) cc_final: 0.8221 (t-100) REVERT: A 689 LYS cc_start: 0.8592 (ptmt) cc_final: 0.8329 (ptmt) REVERT: A 696 ASN cc_start: 0.8012 (t0) cc_final: 0.7717 (t0) REVERT: A 881 GLU cc_start: 0.8691 (tt0) cc_final: 0.8219 (mt-10) REVERT: B 262 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: B 339 THR cc_start: 0.8716 (t) cc_final: 0.8428 (m) REVERT: B 441 MET cc_start: 0.8324 (mmm) cc_final: 0.8043 (mmp) REVERT: B 507 TRP cc_start: 0.8429 (t-100) cc_final: 0.8205 (t-100) REVERT: B 689 LYS cc_start: 0.8595 (ptmt) cc_final: 0.8329 (ptmt) REVERT: B 696 ASN cc_start: 0.8001 (t0) cc_final: 0.7706 (t0) REVERT: B 881 GLU cc_start: 0.8682 (tt0) cc_final: 0.8210 (mt-10) REVERT: C 262 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: C 339 THR cc_start: 0.8720 (t) cc_final: 0.8436 (m) REVERT: C 441 MET cc_start: 0.8323 (mmm) cc_final: 0.8042 (mmp) REVERT: C 507 TRP cc_start: 0.8441 (t-100) cc_final: 0.8217 (t-100) REVERT: C 689 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8314 (ptmt) REVERT: C 696 ASN cc_start: 0.8014 (t0) cc_final: 0.7719 (t0) REVERT: C 881 GLU cc_start: 0.8693 (tt0) cc_final: 0.8222 (mt-10) REVERT: D 262 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: D 339 THR cc_start: 0.8722 (t) cc_final: 0.8440 (m) REVERT: D 441 MET cc_start: 0.8313 (mmm) cc_final: 0.8033 (mmp) REVERT: D 507 TRP cc_start: 0.8440 (t-100) cc_final: 0.8217 (t-100) REVERT: D 689 LYS cc_start: 0.8592 (ptmt) cc_final: 0.8330 (ptmt) REVERT: D 696 ASN cc_start: 0.8010 (t0) cc_final: 0.7714 (t0) REVERT: D 881 GLU cc_start: 0.8688 (tt0) cc_final: 0.8218 (mt-10) outliers start: 43 outliers final: 20 residues processed: 324 average time/residue: 0.3599 time to fit residues: 184.4153 Evaluate side-chains 324 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 300 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 220 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 271 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN B 316 ASN C 338 ASN D 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.156329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118539 restraints weight = 25317.615| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.08 r_work: 0.3258 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23816 Z= 0.154 Angle : 0.505 7.140 32300 Z= 0.262 Chirality : 0.039 0.136 3684 Planarity : 0.004 0.036 3956 Dihedral : 8.253 69.573 4076 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.60 % Allowed : 11.70 % Favored : 86.70 % 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: -0.13 (0.16), residues: 2904 helix: 0.69 (0.12), residues: 1924 sheet: None (None), residues: 0 loop : -1.59 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 514 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE D 548 TYR 0.010 0.001 TYR B 209 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 1240) hydrogen bonds : angle 3.02336 ( 3660) SS BOND : bond 0.01129 ( 4) SS BOND : angle 3.43093 ( 8) covalent geometry : bond 0.00387 (23812) covalent geometry : angle 0.50198 (32292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 2.829 Fit side-chains REVERT: A 262 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: A 339 THR cc_start: 0.8748 (t) cc_final: 0.8457 (m) REVERT: A 437 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8042 (ttm-80) REVERT: A 441 MET cc_start: 0.8339 (mmm) cc_final: 0.8048 (mmp) REVERT: A 507 TRP cc_start: 0.8440 (t-100) cc_final: 0.8229 (t-100) REVERT: A 689 LYS cc_start: 0.8615 (ptmt) cc_final: 0.8331 (ptmt) REVERT: A 696 ASN cc_start: 0.7984 (t0) cc_final: 0.7681 (t0) REVERT: A 881 GLU cc_start: 0.8722 (tt0) cc_final: 0.8127 (mt-10) REVERT: B 262 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: B 339 THR cc_start: 0.8744 (t) cc_final: 0.8454 (m) REVERT: B 437 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8041 (ttm-80) REVERT: B 441 MET cc_start: 0.8349 (mmm) cc_final: 0.8060 (mmp) REVERT: B 507 TRP cc_start: 0.8431 (t-100) cc_final: 0.8221 (t-100) REVERT: B 689 LYS cc_start: 0.8617 (ptmt) cc_final: 0.8330 (ptmt) REVERT: B 696 ASN cc_start: 0.7976 (t0) cc_final: 0.7672 (t0) REVERT: B 881 GLU cc_start: 0.8719 (tt0) cc_final: 0.8121 (mt-10) REVERT: C 262 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: C 339 THR cc_start: 0.8755 (t) cc_final: 0.8464 (m) REVERT: C 437 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: C 441 MET cc_start: 0.8347 (mmm) cc_final: 0.8060 (mmp) REVERT: C 507 TRP cc_start: 0.8441 (t-100) cc_final: 0.8230 (t-100) REVERT: C 689 LYS cc_start: 0.8606 (ptmt) cc_final: 0.8316 (ptmt) REVERT: C 696 ASN cc_start: 0.7993 (t0) cc_final: 0.7689 (t0) REVERT: C 881 GLU cc_start: 0.8715 (tt0) cc_final: 0.8119 (mt-10) REVERT: D 262 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: D 339 THR cc_start: 0.8749 (t) cc_final: 0.8461 (m) REVERT: D 437 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8063 (ttm-80) REVERT: D 441 MET cc_start: 0.8340 (mmm) cc_final: 0.8050 (mmp) REVERT: D 507 TRP cc_start: 0.8437 (t-100) cc_final: 0.8226 (t-100) REVERT: D 689 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8327 (ptmt) REVERT: D 696 ASN cc_start: 0.7991 (t0) cc_final: 0.7685 (t0) REVERT: D 881 GLU cc_start: 0.8717 (tt0) cc_final: 0.8120 (mt-10) outliers start: 36 outliers final: 28 residues processed: 332 average time/residue: 0.3611 time to fit residues: 187.5083 Evaluate side-chains 336 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 304 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2991 > 50: distance: 97 - 116: 29.685 distance: 112 - 116: 32.392 distance: 116 - 117: 5.564 distance: 117 - 118: 57.937 distance: 117 - 120: 40.294 distance: 118 - 119: 38.814 distance: 120 - 121: 56.520 distance: 121 - 122: 38.896 distance: 122 - 124: 39.853 distance: 129 - 130: 39.579 distance: 129 - 133: 56.084 distance: 133 - 134: 40.483 distance: 134 - 137: 23.967 distance: 135 - 136: 34.205 distance: 135 - 145: 33.942 distance: 137 - 138: 25.551 distance: 139 - 141: 18.549 distance: 141 - 143: 3.253 distance: 142 - 143: 24.148 distance: 143 - 144: 23.980 distance: 145 - 146: 39.398 distance: 146 - 147: 20.698 distance: 146 - 149: 25.294 distance: 147 - 148: 21.695 distance: 147 - 156: 12.785 distance: 150 - 151: 18.518 distance: 150 - 152: 41.050 distance: 151 - 153: 20.983 distance: 152 - 154: 41.182 distance: 153 - 155: 46.721 distance: 154 - 155: 30.409 distance: 156 - 157: 45.427 distance: 158 - 165: 34.269 distance: 160 - 161: 39.049 distance: 161 - 162: 39.253 distance: 162 - 163: 34.539 distance: 162 - 164: 54.051 distance: 165 - 166: 54.237 distance: 166 - 167: 42.509 distance: 166 - 169: 39.328 distance: 167 - 168: 38.805 distance: 167 - 170: 14.362 distance: 171 - 172: 40.618 distance: 172 - 173: 51.954 distance: 172 - 174: 54.452 distance: 174 - 175: 32.276 distance: 175 - 176: 42.036 distance: 175 - 178: 53.223 distance: 176 - 177: 48.184 distance: 176 - 185: 35.071 distance: 180 - 181: 30.913 distance: 181 - 182: 35.492 distance: 182 - 183: 5.786 distance: 182 - 184: 13.253 distance: 185 - 186: 17.377 distance: 186 - 187: 22.938 distance: 186 - 189: 43.056 distance: 187 - 188: 19.844 distance: 187 - 192: 24.131 distance: 189 - 190: 5.038 distance: 189 - 191: 39.124 distance: 192 - 193: 56.003 distance: 193 - 194: 40.079 distance: 193 - 196: 40.886 distance: 194 - 195: 40.780 distance: 194 - 200: 34.617 distance: 197 - 199: 41.896