Starting phenix.real_space_refine on Sat Jun 6 06:33:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y09_72389/06_2026/9y09_72389.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y09_72389/06_2026/9y09_72389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y09_72389/06_2026/9y09_72389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y09_72389/06_2026/9y09_72389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y09_72389/06_2026/9y09_72389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y09_72389/06_2026/9y09_72389.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.020 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 P 36 5.49 5 Mg 12 5.21 5 S 144 5.16 5 C 16254 2.51 5 N 4566 2.21 5 O 4986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25998 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "B" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "C" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "D" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "E" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "F" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.55, per 1000 atoms: 0.21 Number of scatterers: 25998 At special positions: 0 Unit cell: (138, 145, 96, 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) S 144 16.00 P 36 15.00 Mg 12 11.99 O 4986 8.00 N 4566 7.00 C 16254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 12 sheets defined 57.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.293A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.308A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.576A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.624A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.053A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.828A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.664A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.207A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.808A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 550 removed outlier: 3.527A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 Processing helix chain 'A' and resid 578 through 584 removed outlier: 4.086A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.354A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.559A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 683 through 707 removed outlier: 3.590A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.773A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.237A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.321A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.557A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.709A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.123A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.809A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 339 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.053A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 359' Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.500A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.287A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.838A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.627A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 4.133A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 4.102A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.505A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 678 removed outlier: 3.933A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 707 removed outlier: 3.583A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.970A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.222A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.227A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.600A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.665A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.020A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.676A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.658A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.197A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.912A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 557 through 569 Processing helix chain 'C' and resid 578 through 584 removed outlier: 4.075A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 4.322A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.545A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 678 removed outlier: 3.930A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.507A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.818A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 226 removed outlier: 4.285A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.310A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.541A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.730A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.058A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.822A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.668A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.199A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.827A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 550 removed outlier: 3.538A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 Processing helix chain 'D' and resid 578 through 584 removed outlier: 4.086A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 610 removed outlier: 4.350A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.568A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 683 through 707 removed outlier: 3.574A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.765A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.234A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.317A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.569A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.721A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.131A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.822A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.666A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 425 removed outlier: 3.511A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.279A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.852A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 544 through 550 Processing helix chain 'E' and resid 556 through 569 removed outlier: 4.621A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 584 removed outlier: 4.128A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 4.151A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.555A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 678 removed outlier: 4.044A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 676 " --> pdb=" O LEU E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 707 removed outlier: 3.606A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.921A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 210 through 226 removed outlier: 4.241A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.225A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.578A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.598A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.024A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.662A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 339 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.653A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 448 through 456 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.193A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.907A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 544 through 550 Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.585A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 removed outlier: 4.070A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 4.306A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.527A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 678 removed outlier: 3.942A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 707 removed outlier: 3.522A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.844A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.180A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.539A pdb=" N GLU A 470 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.183A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.540A pdb=" N GLU B 470 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.289A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.604A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.191A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 469 through 470 removed outlier: 3.535A pdb=" N GLU D 470 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.170A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 469 through 470 removed outlier: 3.536A pdb=" N GLU E 470 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.291A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 469 through 470 removed outlier: 6.599A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1235 hydrogen bonds defined for protein. 3480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 8999 1.37 - 1.52: 7417 1.52 - 1.66: 9780 1.66 - 1.80: 184 1.80 - 1.95: 50 Bond restraints: 26430 Sorted by residual: bond pdb=" CG PRO D 237 " pdb=" CD PRO D 237 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.16e+00 bond pdb=" CA ILE C 303 " pdb=" CB ILE C 303 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.04e+00 bond pdb=" CA ILE F 303 " pdb=" CB ILE F 303 " ideal model delta sigma weight residual 1.540 1.527 0.014 1.36e-02 5.41e+03 9.95e-01 bond pdb=" CB PRO B 237 " pdb=" CG PRO B 237 " ideal model delta sigma weight residual 1.492 1.541 -0.049 5.00e-02 4.00e+02 9.76e-01 bond pdb=" CB PRO E 237 " pdb=" CG PRO E 237 " ideal model delta sigma weight residual 1.492 1.541 -0.049 5.00e-02 4.00e+02 9.59e-01 ... (remaining 26425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 34922 1.53 - 3.06: 671 3.06 - 4.59: 121 4.59 - 6.12: 28 6.12 - 7.65: 12 Bond angle restraints: 35754 Sorted by residual: angle pdb=" C ARG D 599 " pdb=" CA ARG D 599 " pdb=" CB ARG D 599 " ideal model delta sigma weight residual 117.23 109.68 7.55 1.36e+00 5.41e-01 3.09e+01 angle pdb=" C ARG A 599 " pdb=" CA ARG A 599 " pdb=" CB ARG A 599 " ideal model delta sigma weight residual 117.23 109.74 7.49 1.36e+00 5.41e-01 3.03e+01 angle pdb=" C ARG B 599 " pdb=" CA ARG B 599 " pdb=" CB ARG B 599 " ideal model delta sigma weight residual 117.23 109.97 7.26 1.36e+00 5.41e-01 2.85e+01 angle pdb=" N VAL C 441 " pdb=" CA VAL C 441 " pdb=" C VAL C 441 " ideal model delta sigma weight residual 113.22 107.70 5.52 1.23e+00 6.61e-01 2.01e+01 angle pdb=" N VAL F 441 " pdb=" CA VAL F 441 " pdb=" C VAL F 441 " ideal model delta sigma weight residual 113.22 107.78 5.44 1.23e+00 6.61e-01 1.95e+01 ... (remaining 35749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 14927 17.76 - 35.53: 1111 35.53 - 53.29: 257 53.29 - 71.06: 39 71.06 - 88.82: 16 Dihedral angle restraints: 16350 sinusoidal: 6912 harmonic: 9438 Sorted by residual: dihedral pdb=" CA ALA C 297 " pdb=" C ALA C 297 " pdb=" N PRO C 298 " pdb=" CA PRO C 298 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ALA E 297 " pdb=" C ALA E 297 " pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 16347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2378 0.029 - 0.059: 1041 0.059 - 0.088: 344 0.088 - 0.118: 231 0.118 - 0.147: 26 Chirality restraints: 4020 Sorted by residual: chirality pdb=" CA ILE E 300 " pdb=" N ILE E 300 " pdb=" C ILE E 300 " pdb=" CB ILE E 300 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE D 300 " pdb=" N ILE D 300 " pdb=" C ILE D 300 " pdb=" CB ILE D 300 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE B 300 " pdb=" N ILE B 300 " pdb=" C ILE B 300 " pdb=" CB ILE B 300 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 4017 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 460 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO F 461 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 461 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 461 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 460 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO C 461 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 461 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 461 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 460 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO D 461 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 461 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 461 " -0.036 5.00e-02 4.00e+02 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 199 2.54 - 3.13: 20373 3.13 - 3.72: 43274 3.72 - 4.31: 60437 4.31 - 4.90: 95082 Nonbonded interactions: 219365 Sorted by model distance: nonbonded pdb=" OG1 THR F 252 " pdb="MG MG F 903 " model vdw 1.954 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 903 " model vdw 1.954 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 1.962 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 902 " model vdw 1.962 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 903 " model vdw 1.966 2.170 ... (remaining 219360 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 200 through 901 or resid 903)) selection = (chain 'B' and (resid 200 through 901 or resid 903)) selection = (chain 'C' and (resid 200 through 901 or resid 903)) selection = (chain 'D' and (resid 200 through 901 or resid 903)) selection = (chain 'E' and (resid 200 through 901 or resid 903)) selection = (chain 'F' and (resid 200 through 901 or resid 903)) } 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.680 Find NCS groups from input model: 0.650 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: 0.000 Load rotamer database and sin/cos tables:8.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26436 Z= 0.114 Angle : 0.555 7.653 35754 Z= 0.297 Chirality : 0.042 0.147 4020 Planarity : 0.005 0.067 4668 Dihedral : 13.364 88.819 10230 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.21 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3270 helix: 0.44 (0.13), residues: 1698 sheet: 0.10 (0.26), residues: 378 loop : 0.70 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 256 TYR 0.011 0.001 TYR D 244 PHE 0.008 0.001 PHE A 506 TRP 0.036 0.004 TRP D 551 HIS 0.012 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (26430) covalent geometry : angle 0.55526 / 0.30 (35754) hydrogen bonds : bond 0.20656 / 13.89 ( 1235) hydrogen bonds : angle 6.02258 / 4.38 ( 3480) Misc. bond : bond 0.00072 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 LYS cc_start: 0.9152 (ttmt) cc_final: 0.8918 (ttmt) REVERT: A 397 GLU cc_start: 0.8660 (tt0) cc_final: 0.8319 (tp30) REVERT: A 398 GLN cc_start: 0.9025 (tp-100) cc_final: 0.8628 (tp-100) REVERT: B 305 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8667 (mt-10) REVERT: B 340 HIS cc_start: 0.8410 (m-70) cc_final: 0.8170 (m90) REVERT: B 352 SER cc_start: 0.9231 (m) cc_final: 0.9019 (p) REVERT: B 389 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8889 (ttmt) REVERT: B 689 GLU cc_start: 0.8529 (tp30) cc_final: 0.8308 (tp30) REVERT: C 352 SER cc_start: 0.9326 (m) cc_final: 0.9023 (t) REVERT: C 426 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8022 (mmtm) REVERT: C 470 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8036 (pt0) REVERT: C 564 ASP cc_start: 0.8628 (m-30) cc_final: 0.8252 (m-30) REVERT: C 651 LYS cc_start: 0.8856 (tttp) cc_final: 0.8596 (mppt) REVERT: D 397 GLU cc_start: 0.8646 (tt0) cc_final: 0.8362 (tp30) REVERT: D 398 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8665 (tp-100) REVERT: E 239 ARG cc_start: 0.7273 (ptt180) cc_final: 0.6958 (pmm-80) REVERT: E 305 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8716 (mt-10) REVERT: E 340 HIS cc_start: 0.8423 (m-70) cc_final: 0.8152 (m90) REVERT: E 352 SER cc_start: 0.9245 (m) cc_final: 0.9033 (p) REVERT: E 389 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8882 (ttmt) REVERT: E 397 GLU cc_start: 0.8684 (tt0) cc_final: 0.8347 (tp30) REVERT: E 689 GLU cc_start: 0.8497 (tp30) cc_final: 0.8269 (tp30) REVERT: F 352 SER cc_start: 0.9327 (m) cc_final: 0.9042 (t) REVERT: F 397 GLU cc_start: 0.8613 (tt0) cc_final: 0.8306 (tp30) REVERT: F 426 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8073 (mmtm) REVERT: F 470 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8131 (pt0) REVERT: F 564 ASP cc_start: 0.8713 (m-30) cc_final: 0.8444 (m-30) REVERT: F 651 LYS cc_start: 0.8856 (tttp) cc_final: 0.8592 (mppt) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.8821 time to fit residues: 604.4365 Evaluate side-chains 315 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 568 GLN B 226 HIS B 337 GLN B 460 ASN B 499 HIS B 568 GLN B 603 GLN B 660 ASN B 692 GLN C 226 HIS C 285 ASN C 337 GLN C 494 GLN C 499 HIS C 568 GLN D 337 GLN D 568 GLN E 226 HIS ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 GLN E 499 HIS E 568 GLN E 603 GLN E 660 ASN E 692 GLN F 226 HIS F 285 ASN F 337 GLN F 494 GLN F 499 HIS F 568 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093678 restraints weight = 36368.117| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.69 r_work: 0.3016 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26436 Z= 0.155 Angle : 0.617 9.686 35754 Z= 0.311 Chirality : 0.044 0.185 4020 Planarity : 0.005 0.068 4668 Dihedral : 8.973 59.819 3780 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.76 % Favored : 95.87 % Rotamer: Outliers : 2.78 % Allowed : 11.17 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3270 helix: 0.73 (0.13), residues: 1698 sheet: 0.09 (0.26), residues: 378 loop : 0.83 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 256 TYR 0.016 0.002 TYR B 203 PHE 0.019 0.001 PHE C 742 TRP 0.025 0.003 TRP A 551 HIS 0.008 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (26430) covalent geometry : angle 0.61734 / 0.31 (35754) hydrogen bonds : bond 0.04686 / 3.14 ( 1235) hydrogen bonds : angle 4.27076 / 3.07 ( 3480) Misc. bond : bond 0.00256 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 342 time to evaluate : 1.010 Fit side-chains REVERT: A 389 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8869 (ttmt) REVERT: A 397 GLU cc_start: 0.8694 (tt0) cc_final: 0.8294 (tp30) REVERT: B 203 TYR cc_start: 0.8256 (m-10) cc_final: 0.8003 (m-80) REVERT: B 340 HIS cc_start: 0.8402 (m-70) cc_final: 0.8190 (m90) REVERT: B 389 LYS cc_start: 0.9158 (ttmt) cc_final: 0.8899 (ttmt) REVERT: B 689 GLU cc_start: 0.8418 (tp30) cc_final: 0.8204 (tp30) REVERT: B 701 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8276 (mt-10) REVERT: B 764 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6891 (mt0) REVERT: C 352 SER cc_start: 0.9307 (m) cc_final: 0.9055 (t) REVERT: C 402 GLU cc_start: 0.8633 (tt0) cc_final: 0.8395 (mt-10) REVERT: C 426 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7851 (mtpt) REVERT: C 470 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8082 (pt0) REVERT: C 564 ASP cc_start: 0.8684 (m-30) cc_final: 0.8426 (m-30) REVERT: D 309 ILE cc_start: 0.8971 (pt) cc_final: 0.8754 (pt) REVERT: D 319 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: D 397 GLU cc_start: 0.8610 (tt0) cc_final: 0.8259 (tp30) REVERT: D 701 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8176 (mt-10) REVERT: D 764 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: E 340 HIS cc_start: 0.8360 (m-70) cc_final: 0.8088 (m90) REVERT: E 389 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8922 (ttmt) REVERT: E 397 GLU cc_start: 0.8517 (tt0) cc_final: 0.8217 (tp30) REVERT: E 689 GLU cc_start: 0.8412 (tp30) cc_final: 0.8201 (tp30) REVERT: E 701 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8264 (mt-10) REVERT: E 764 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6902 (mt0) REVERT: F 321 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8278 (mt-10) REVERT: F 352 SER cc_start: 0.9312 (m) cc_final: 0.9066 (t) REVERT: F 402 GLU cc_start: 0.8616 (tt0) cc_final: 0.8357 (mt-10) REVERT: F 426 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7819 (mtpt) REVERT: F 701 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8135 (mt-10) outliers start: 76 outliers final: 40 residues processed: 397 average time/residue: 0.7430 time to fit residues: 335.5352 Evaluate side-chains 336 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 GLN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 693 ARG Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 693 ARG Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 693 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 292 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 494 GLN B 226 HIS B 327 GLN B 398 GLN C 226 HIS C 327 GLN D 285 ASN D 327 GLN D 494 GLN E 226 HIS E 327 GLN E 398 GLN F 226 HIS F 327 GLN F 337 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.088810 restraints weight = 36453.855| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.69 r_work: 0.2931 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26436 Z= 0.219 Angle : 0.647 9.228 35754 Z= 0.323 Chirality : 0.046 0.165 4020 Planarity : 0.006 0.068 4668 Dihedral : 9.027 63.365 3780 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.01 % Favored : 95.66 % Rotamer: Outliers : 3.11 % Allowed : 12.67 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 3270 helix: 0.75 (0.13), residues: 1740 sheet: -0.26 (0.24), residues: 396 loop : 0.90 (0.21), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 256 TYR 0.015 0.002 TYR C 244 PHE 0.013 0.002 PHE F 758 TRP 0.020 0.003 TRP A 551 HIS 0.006 0.001 HIS E 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (26430) covalent geometry : angle 0.64702 / 0.32 (35754) hydrogen bonds : bond 0.04406 / 2.96 ( 1235) hydrogen bonds : angle 3.99332 / 2.85 ( 3480) Misc. bond : bond 0.00292 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 293 time to evaluate : 1.016 Fit side-chains REVERT: A 389 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8869 (ttmt) REVERT: A 397 GLU cc_start: 0.8648 (tt0) cc_final: 0.8164 (tp30) REVERT: A 704 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: B 389 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8938 (ttmt) REVERT: B 764 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7077 (mt0) REVERT: C 352 SER cc_start: 0.9326 (m) cc_final: 0.9071 (t) REVERT: C 402 GLU cc_start: 0.8630 (tt0) cc_final: 0.8405 (mt-10) REVERT: C 470 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8122 (pt0) REVERT: C 704 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: D 309 ILE cc_start: 0.9011 (pt) cc_final: 0.8780 (pt) REVERT: D 397 GLU cc_start: 0.8638 (tt0) cc_final: 0.8185 (tp30) REVERT: D 701 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8117 (mt-10) REVERT: D 704 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: D 764 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: E 389 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8939 (ttmt) REVERT: E 397 GLU cc_start: 0.8534 (tt0) cc_final: 0.8152 (tp30) REVERT: E 561 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8385 (mt-10) REVERT: E 704 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: E 764 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7072 (mt0) REVERT: F 352 SER cc_start: 0.9323 (m) cc_final: 0.9065 (t) REVERT: F 402 GLU cc_start: 0.8657 (tt0) cc_final: 0.8431 (mt-10) REVERT: F 426 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7968 (mtpt) REVERT: F 704 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7842 (mp0) outliers start: 85 outliers final: 43 residues processed: 355 average time/residue: 0.8039 time to fit residues: 322.3507 Evaluate side-chains 314 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 704 GLU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 103 optimal weight: 3.9990 chunk 323 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 297 optimal weight: 0.2980 chunk 244 optimal weight: 0.0170 chunk 266 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 603 GLN F 660 ASN F 764 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091385 restraints weight = 36199.483| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.68 r_work: 0.2980 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26436 Z= 0.125 Angle : 0.572 9.210 35754 Z= 0.285 Chirality : 0.042 0.149 4020 Planarity : 0.005 0.069 4668 Dihedral : 8.692 56.691 3780 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.73 % Favored : 95.93 % Rotamer: Outliers : 2.93 % Allowed : 14.21 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3270 helix: 1.00 (0.13), residues: 1746 sheet: -0.19 (0.25), residues: 378 loop : 0.96 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 256 TYR 0.011 0.001 TYR F 244 PHE 0.010 0.001 PHE F 302 TRP 0.011 0.002 TRP A 551 HIS 0.002 0.000 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (26430) covalent geometry : angle 0.57197 / 0.28 (35754) hydrogen bonds : bond 0.03542 / 2.38 ( 1235) hydrogen bonds : angle 3.93418 / 2.80 ( 3480) Misc. bond : bond 0.00069 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 278 time to evaluate : 1.013 Fit side-chains REVERT: A 389 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8868 (ttmt) REVERT: A 397 GLU cc_start: 0.8608 (tt0) cc_final: 0.8153 (tp30) REVERT: A 668 LYS cc_start: 0.8928 (mmpt) cc_final: 0.8690 (mmpt) REVERT: B 389 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8942 (ttmt) REVERT: B 668 LYS cc_start: 0.9118 (mmpt) cc_final: 0.8915 (mmpt) REVERT: B 764 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: C 292 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8124 (mm-30) REVERT: C 352 SER cc_start: 0.9302 (m) cc_final: 0.9032 (t) REVERT: C 358 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8447 (mtt180) REVERT: C 470 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8087 (pt0) REVERT: C 764 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7054 (mt0) REVERT: D 309 ILE cc_start: 0.8898 (pt) cc_final: 0.8630 (pt) REVERT: D 321 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8305 (mt-10) REVERT: D 397 GLU cc_start: 0.8605 (tt0) cc_final: 0.8164 (tp30) REVERT: D 701 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8020 (mt-10) REVERT: D 764 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: E 389 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8946 (ttmt) REVERT: E 397 GLU cc_start: 0.8514 (tt0) cc_final: 0.8164 (tp30) REVERT: E 427 MET cc_start: 0.6384 (mmp) cc_final: 0.6105 (mmp) REVERT: E 561 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8388 (mt-10) REVERT: E 668 LYS cc_start: 0.8948 (mmpt) cc_final: 0.8618 (mmpt) REVERT: E 764 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: F 352 SER cc_start: 0.9313 (m) cc_final: 0.9046 (t) REVERT: F 358 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8432 (mtt180) REVERT: F 402 GLU cc_start: 0.8649 (tt0) cc_final: 0.8417 (mt-10) REVERT: F 426 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8073 (mtpt) REVERT: F 668 LYS cc_start: 0.9210 (mmpt) cc_final: 0.8954 (mmpt) outliers start: 80 outliers final: 40 residues processed: 335 average time/residue: 0.8356 time to fit residues: 314.5030 Evaluate side-chains 304 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 764 GLN Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 677 LYS Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 677 LYS Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8339 > 50: distance: 31 - 52: 34.529 distance: 36 - 57: 30.179 distance: 44 - 65: 33.705 distance: 47 - 52: 34.653 distance: 48 - 74: 34.551 distance: 53 - 54: 56.881 distance: 54 - 57: 33.937 distance: 57 - 58: 40.886 distance: 58 - 59: 56.899 distance: 58 - 61: 41.496 distance: 59 - 60: 39.482 distance: 59 - 65: 40.566 distance: 61 - 62: 55.522 distance: 62 - 64: 68.056 distance: 66 - 69: 39.170 distance: 67 - 68: 56.451 distance: 69 - 70: 40.156 distance: 70 - 71: 56.308 distance: 71 - 72: 55.914 distance: 74 - 75: 41.042 distance: 78 - 79: 40.601 distance: 91 - 92: 38.995 distance: 94 - 95: 40.847 distance: 95 - 96: 38.970 distance: 98 - 100: 39.632 distance: 102 - 105: 40.453 distance: 103 - 104: 41.073 distance: 105 - 106: 40.428 distance: 112 - 113: 40.011 distance: 113 - 114: 39.640 distance: 113 - 116: 47.035 distance: 116 - 117: 31.940 distance: 117 - 118: 21.082 distance: 117 - 119: 17.877 distance: 120 - 122: 38.906 distance: 125 - 126: 57.095 distance: 125 - 131: 34.555 distance: 127 - 128: 55.636 distance: 128 - 130: 40.953