Starting phenix.real_space_refine on Sat Feb 7 15:50:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rlh_24530/02_2026/7rlh_24530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlh_24530/02_2026/7rlh_24530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rlh_24530/02_2026/7rlh_24530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlh_24530/02_2026/7rlh_24530.map" model { file = "/net/cci-nas-00/data/ceres_data/7rlh_24530/02_2026/7rlh_24530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlh_24530/02_2026/7rlh_24530.cif" } resolution = 3.0 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= 0.054 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 192 5.16 5 C 21636 2.51 5 N 6096 2.21 5 O 6612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34584 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} 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} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 6.90, per 1000 atoms: 0.20 Number of scatterers: 34584 At special positions: 0 Unit cell: (169, 173, 97, 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 192 16.00 P 36 15.00 Mg 12 11.99 O 6612 8.00 N 6096 7.00 C 21636 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 24 sheets defined 48.1% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.574A pdb=" N MET A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.779A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.668A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.566A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 5.037A 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 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.154A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 349 through 353 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 428 removed outlier: 3.993A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.647A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.075A 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: 3.830A 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 551 Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 555 through 569 removed outlier: 4.454A pdb=" N VAL A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 removed outlier: 3.911A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.968A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.571A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 707 removed outlier: 3.501A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.578A 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 42 through 49 removed outlier: 3.574A pdb=" N MET B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.779A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.665A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 5.036A 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 Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.153A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 336 through 339 Processing helix chain 'B' and resid 349 through 353 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 428 removed outlier: 3.993A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.647A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.073A 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 507 removed outlier: 3.831A 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 551 Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 555 through 569 removed outlier: 4.455A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 3.911A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.968A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.572A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 707 removed outlier: 3.501A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.576A 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 42 through 49 removed outlier: 3.575A pdb=" N MET C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.778A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.667A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 removed outlier: 5.037A 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 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.152A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 336 through 339 Processing helix chain 'C' and resid 349 through 353 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 428 removed outlier: 3.993A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.646A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.075A 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 507 removed outlier: 3.831A 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 551 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 555 through 569 removed outlier: 4.454A pdb=" N VAL C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 584 removed outlier: 3.912A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 3.968A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.572A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.501A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.577A 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 42 through 49 removed outlier: 3.574A pdb=" N MET D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.779A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.667A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.566A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 226 removed outlier: 5.037A 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 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.154A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 349 through 353 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 428 removed outlier: 3.993A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.647A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.075A 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 507 removed outlier: 3.831A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 544 through 551 Processing helix chain 'D' and resid 552 through 554 No H-bonds generated for 'chain 'D' and resid 552 through 554' Processing helix chain 'D' and resid 555 through 569 removed outlier: 4.456A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 removed outlier: 3.912A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 610 removed outlier: 3.969A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.573A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 707 removed outlier: 3.501A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.578A 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 42 through 49 removed outlier: 3.573A pdb=" N MET E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.779A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.668A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 226 removed outlier: 5.036A 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 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.152A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 349 through 353 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 428 removed outlier: 3.993A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.647A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.075A 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 507 removed outlier: 3.831A 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 551 Processing helix chain 'E' and resid 552 through 554 No H-bonds generated for 'chain 'E' and resid 552 through 554' Processing helix chain 'E' and resid 555 through 569 removed outlier: 4.455A pdb=" N VAL E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 584 removed outlier: 3.912A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 3.969A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.572A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 707 removed outlier: 3.501A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.576A 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 42 through 49 removed outlier: 3.575A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.780A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.667A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 226 removed outlier: 5.037A 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 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.153A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 Processing helix chain 'F' and resid 336 through 339 Processing helix chain 'F' and resid 349 through 353 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 428 removed outlier: 3.994A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.646A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.074A 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 507 removed outlier: 3.831A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 544 through 551 Processing helix chain 'F' and resid 552 through 554 No H-bonds generated for 'chain 'F' and resid 552 through 554' Processing helix chain 'F' and resid 555 through 569 removed outlier: 4.455A pdb=" N VAL F 559 " --> pdb=" O SER F 555 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 removed outlier: 3.911A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.968A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.572A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 707 removed outlier: 3.502A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.577A 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 25 through 30 removed outlier: 8.022A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 118 removed outlier: 6.157A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.409A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.661A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 30 removed outlier: 8.022A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 118 removed outlier: 6.157A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.410A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.662A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.022A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.157A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.409A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.662A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 30 removed outlier: 8.023A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 114 through 118 removed outlier: 6.157A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.407A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.663A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 30 removed outlier: 8.022A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 114 through 118 removed outlier: 6.158A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.410A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 538 through 543 removed outlier: 6.663A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 25 through 30 removed outlier: 8.022A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 114 through 118 removed outlier: 6.158A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.409A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 538 through 543 removed outlier: 6.662A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1412 hydrogen bonds defined for protein. 4092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.34 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11966 1.37 - 1.51: 10079 1.51 - 1.66: 12809 1.66 - 1.80: 251 1.80 - 1.95: 49 Bond restraints: 35154 Sorted by residual: bond pdb=" CD ARG E 662 " pdb=" NE ARG E 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.49e+00 bond pdb=" CD ARG C 662 " pdb=" NE ARG C 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.45e+00 bond pdb=" CD ARG F 662 " pdb=" NE ARG F 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.39e+00 bond pdb=" CD ARG A 662 " pdb=" NE ARG A 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.38e+00 bond pdb=" CD ARG D 662 " pdb=" NE ARG D 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.36e+00 ... (remaining 35149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 46429 1.65 - 3.31: 945 3.31 - 4.96: 128 4.96 - 6.61: 42 6.61 - 8.27: 12 Bond angle restraints: 47556 Sorted by residual: angle pdb=" N TYR B 138 " pdb=" CA TYR B 138 " pdb=" C TYR B 138 " ideal model delta sigma weight residual 114.75 108.88 5.87 1.26e+00 6.30e-01 2.17e+01 angle pdb=" N TYR D 138 " pdb=" CA TYR D 138 " pdb=" C TYR D 138 " ideal model delta sigma weight residual 114.75 108.89 5.86 1.26e+00 6.30e-01 2.17e+01 angle pdb=" N TYR F 138 " pdb=" CA TYR F 138 " pdb=" C TYR F 138 " ideal model delta sigma weight residual 114.75 108.89 5.86 1.26e+00 6.30e-01 2.16e+01 angle pdb=" N TYR A 138 " pdb=" CA TYR A 138 " pdb=" C TYR A 138 " ideal model delta sigma weight residual 114.75 108.90 5.85 1.26e+00 6.30e-01 2.15e+01 angle pdb=" N TYR C 138 " pdb=" CA TYR C 138 " pdb=" C TYR C 138 " ideal model delta sigma weight residual 114.75 108.91 5.84 1.26e+00 6.30e-01 2.15e+01 ... (remaining 47551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 19864 16.75 - 33.49: 1482 33.49 - 50.24: 386 50.24 - 66.98: 48 66.98 - 83.73: 54 Dihedral angle restraints: 21834 sinusoidal: 9264 harmonic: 12570 Sorted by residual: dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N PRO B 298 " pdb=" CA PRO B 298 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 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 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ALA F 297 " pdb=" C ALA F 297 " pdb=" N PRO F 298 " pdb=" CA PRO F 298 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 21831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2915 0.027 - 0.054: 1395 0.054 - 0.081: 585 0.081 - 0.107: 344 0.107 - 0.134: 125 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE F 301 " pdb=" N ILE F 301 " pdb=" C ILE F 301 " pdb=" CB ILE F 301 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE F 371 " pdb=" N ILE F 371 " pdb=" C ILE F 371 " pdb=" CB ILE F 371 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 5361 not shown) Planarity restraints: 6234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 297 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 298 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 297 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO C 298 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 297 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO E 298 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " -0.029 5.00e-02 4.00e+02 ... (remaining 6231 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 154 2.41 - 3.03: 20837 3.03 - 3.65: 54800 3.65 - 4.28: 81550 4.28 - 4.90: 132657 Nonbonded interactions: 289998 Sorted by model distance: nonbonded pdb=" OD1 ASP B 478 " pdb=" NH2 ARG B 662 " model vdw 1.783 3.120 nonbonded pdb=" OD1 ASP E 478 " pdb=" NH2 ARG E 662 " model vdw 1.784 3.120 nonbonded pdb=" OD1 ASP C 478 " pdb=" NH2 ARG C 662 " model vdw 1.784 3.120 nonbonded pdb=" OD1 ASP D 478 " pdb=" NH2 ARG D 662 " model vdw 1.784 3.120 nonbonded pdb=" OD1 ASP F 478 " pdb=" NH2 ARG F 662 " model vdw 1.785 3.120 ... (remaining 289993 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.950 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.970 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.007 0.889 35156 Z= 0.651 Angle : 0.612 8.268 47556 Z= 0.339 Chirality : 0.043 0.134 5364 Planarity : 0.004 0.052 6234 Dihedral : 13.638 83.727 13686 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.05 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.36 (0.14), residues: 4344 helix: 1.04 (0.13), residues: 1884 sheet: 0.20 (0.21), residues: 600 loop : -0.49 (0.16), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 113 TYR 0.018 0.002 TYR E 173 PHE 0.013 0.002 PHE D 267 TRP 0.004 0.001 TRP B 551 HIS 0.007 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00373 (35154) covalent geometry : angle 0.61171 (47556) hydrogen bonds : bond 0.16762 ( 1412) hydrogen bonds : angle 6.13869 ( 4092) Misc. bond : bond 0.83333 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.9082 (mm) cc_final: 0.8879 (mm) REVERT: B 275 MET cc_start: 0.9203 (mmm) cc_final: 0.8989 (mmm) REVERT: C 143 TYR cc_start: 0.8914 (m-80) cc_final: 0.8125 (m-10) REVERT: D 275 MET cc_start: 0.9224 (mmm) cc_final: 0.8981 (mmm) REVERT: E 63 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8115 (tptp) REVERT: F 59 LEU cc_start: 0.9092 (mm) cc_final: 0.8879 (mm) REVERT: F 450 ASP cc_start: 0.8716 (t0) cc_final: 0.8516 (t0) outliers start: 0 outliers final: 2 residues processed: 303 average time/residue: 0.8617 time to fit residues: 303.6953 Evaluate side-chains 178 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain F residue 508 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 0.0060 chunk 155 optimal weight: 20.0000 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN F 760 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.103612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.064360 restraints weight = 77184.998| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.09 r_work: 0.2733 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35156 Z= 0.182 Angle : 0.630 7.861 47556 Z= 0.322 Chirality : 0.046 0.155 5364 Planarity : 0.005 0.063 6234 Dihedral : 7.928 52.228 4986 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.33 % Favored : 95.40 % Rotamer: Outliers : 1.10 % Allowed : 5.84 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.32 (0.14), residues: 4344 helix: 1.10 (0.13), residues: 1854 sheet: 0.02 (0.21), residues: 594 loop : -0.55 (0.16), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 155 TYR 0.011 0.002 TYR F 173 PHE 0.029 0.002 PHE E 139 TRP 0.009 0.001 TRP F 454 HIS 0.004 0.001 HIS E 384 Details of bonding type rmsd covalent geometry : bond 0.00423 (35154) covalent geometry : angle 0.63033 (47556) hydrogen bonds : bond 0.04453 ( 1412) hydrogen bonds : angle 4.75417 ( 4092) Misc. bond : bond 0.00113 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8019 (tpt) cc_final: 0.7808 (tpt) REVERT: A 120 ASP cc_start: 0.8913 (p0) cc_final: 0.8700 (p0) REVERT: A 134 TYR cc_start: 0.8886 (m-80) cc_final: 0.8672 (m-80) REVERT: A 449 MET cc_start: 0.8993 (tpp) cc_final: 0.8780 (tpp) REVERT: A 508 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.4477 (mpt) REVERT: B 135 LEU cc_start: 0.9138 (mp) cc_final: 0.8731 (mp) REVERT: B 146 ILE cc_start: 0.8246 (mp) cc_final: 0.8030 (tp) REVERT: B 151 ILE cc_start: 0.8234 (mm) cc_final: 0.8032 (mm) REVERT: B 561 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: C 84 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7711 (tpt) REVERT: C 143 TYR cc_start: 0.8807 (m-80) cc_final: 0.7988 (m-10) REVERT: D 134 TYR cc_start: 0.8711 (m-80) cc_final: 0.8426 (m-10) REVERT: D 139 PHE cc_start: 0.9226 (m-80) cc_final: 0.8536 (m-80) REVERT: E 63 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8041 (tptp) REVERT: E 139 PHE cc_start: 0.9014 (m-80) cc_final: 0.7799 (m-80) REVERT: F 84 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7875 (tpt) REVERT: F 143 TYR cc_start: 0.8840 (m-80) cc_final: 0.8013 (m-10) REVERT: F 450 ASP cc_start: 0.8792 (t0) cc_final: 0.8537 (t0) outliers start: 41 outliers final: 11 residues processed: 230 average time/residue: 0.6469 time to fit residues: 181.6377 Evaluate side-chains 189 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 263 optimal weight: 4.9990 chunk 415 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 375 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 2 optimal weight: 0.0870 chunk 398 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 57 optimal weight: 0.0470 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS F 458 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.102933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.063458 restraints weight = 77414.204| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.09 r_work: 0.2710 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35156 Z= 0.166 Angle : 0.580 8.971 47556 Z= 0.296 Chirality : 0.045 0.169 5364 Planarity : 0.005 0.054 6234 Dihedral : 7.659 57.283 4986 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.86 % Rotamer: Outliers : 1.21 % Allowed : 7.24 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.38 (0.14), residues: 4344 helix: 1.18 (0.13), residues: 1860 sheet: -0.13 (0.20), residues: 594 loop : -0.47 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 113 TYR 0.015 0.002 TYR B 134 PHE 0.023 0.002 PHE B 139 TRP 0.015 0.002 TRP F 454 HIS 0.003 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00387 (35154) covalent geometry : angle 0.58010 (47556) hydrogen bonds : bond 0.04006 ( 1412) hydrogen bonds : angle 4.45452 ( 4092) Misc. bond : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8049 (tpt) cc_final: 0.7495 (tmm) REVERT: A 115 HIS cc_start: 0.7518 (t-90) cc_final: 0.7208 (t70) REVERT: A 508 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.4569 (mpt) REVERT: B 449 MET cc_start: 0.8944 (tpp) cc_final: 0.8417 (tpp) REVERT: B 561 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: C 143 TYR cc_start: 0.8838 (m-80) cc_final: 0.8023 (m-10) REVERT: D 115 HIS cc_start: 0.7452 (t-90) cc_final: 0.7152 (t70) REVERT: D 139 PHE cc_start: 0.9218 (m-80) cc_final: 0.8525 (m-80) REVERT: D 236 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8985 (mmmm) REVERT: D 449 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8107 (tpp) REVERT: D 508 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.4347 (mpt) REVERT: D 561 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: E 63 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8028 (tptp) REVERT: E 139 PHE cc_start: 0.9025 (m-80) cc_final: 0.7934 (m-80) REVERT: E 449 MET cc_start: 0.8921 (tpp) cc_final: 0.8251 (tpp) REVERT: E 561 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: F 143 TYR cc_start: 0.8816 (m-80) cc_final: 0.7992 (m-10) REVERT: F 449 MET cc_start: 0.9002 (tpt) cc_final: 0.8770 (tpp) REVERT: F 508 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.4483 (mpt) outliers start: 45 outliers final: 21 residues processed: 224 average time/residue: 0.6342 time to fit residues: 174.1941 Evaluate side-chains 205 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 286 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 425 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 405 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.101203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061661 restraints weight = 76982.752| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.07 r_work: 0.2660 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35156 Z= 0.235 Angle : 0.614 8.860 47556 Z= 0.313 Chirality : 0.047 0.205 5364 Planarity : 0.005 0.087 6234 Dihedral : 7.782 56.208 4986 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.49 % Rotamer: Outliers : 1.37 % Allowed : 8.86 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.32 (0.14), residues: 4344 helix: 1.22 (0.13), residues: 1854 sheet: -0.24 (0.20), residues: 606 loop : -0.58 (0.16), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 766 TYR 0.014 0.002 TYR F 203 PHE 0.025 0.002 PHE B 139 TRP 0.013 0.002 TRP F 454 HIS 0.004 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00550 (35154) covalent geometry : angle 0.61394 (47556) hydrogen bonds : bond 0.04123 ( 1412) hydrogen bonds : angle 4.34331 ( 4092) Misc. bond : bond 0.00354 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8167 (tpt) cc_final: 0.7792 (tmm) REVERT: A 115 HIS cc_start: 0.7486 (t-90) cc_final: 0.7122 (t70) REVERT: A 508 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.4633 (mpt) REVERT: B 561 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: B 586 ARG cc_start: 0.3795 (mtt-85) cc_final: 0.3308 (mtp85) REVERT: C 143 TYR cc_start: 0.8852 (m-80) cc_final: 0.8049 (m-10) REVERT: D 139 PHE cc_start: 0.9216 (m-80) cc_final: 0.8551 (m-80) REVERT: D 508 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.4494 (mpt) REVERT: D 561 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: D 586 ARG cc_start: 0.3516 (mtt-85) cc_final: 0.3257 (mtp85) REVERT: E 63 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8025 (tptp) REVERT: E 139 PHE cc_start: 0.9096 (m-80) cc_final: 0.7944 (m-80) REVERT: E 449 MET cc_start: 0.8931 (tpp) cc_final: 0.8289 (tpp) REVERT: E 508 MET cc_start: 0.6009 (mmt) cc_final: 0.5440 (mmt) REVERT: E 561 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: E 586 ARG cc_start: 0.3860 (mtt-85) cc_final: 0.3335 (mtp85) REVERT: F 143 TYR cc_start: 0.8831 (m-80) cc_final: 0.8054 (m-10) REVERT: F 449 MET cc_start: 0.9019 (tpt) cc_final: 0.8794 (tpp) REVERT: F 508 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.4660 (mpt) outliers start: 51 outliers final: 25 residues processed: 235 average time/residue: 0.6066 time to fit residues: 175.8394 Evaluate side-chains 203 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 258 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 364 optimal weight: 20.0000 chunk 417 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 345 optimal weight: 0.3980 chunk 356 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS B 33 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.102290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.062820 restraints weight = 77200.185| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.10 r_work: 0.2691 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35156 Z= 0.143 Angle : 0.563 9.404 47556 Z= 0.286 Chirality : 0.044 0.164 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.592 57.997 4986 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.03 % Favored : 95.70 % Rotamer: Outliers : 1.43 % Allowed : 10.72 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.41 (0.14), residues: 4344 helix: 1.29 (0.13), residues: 1860 sheet: -0.24 (0.20), residues: 594 loop : -0.51 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 113 TYR 0.010 0.001 TYR F 138 PHE 0.012 0.001 PHE A 552 TRP 0.014 0.001 TRP F 454 HIS 0.002 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00332 (35154) covalent geometry : angle 0.56312 (47556) hydrogen bonds : bond 0.03576 ( 1412) hydrogen bonds : angle 4.19722 ( 4092) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8210 (ttp) cc_final: 0.7943 (pp-130) REVERT: A 449 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8117 (tpp) REVERT: A 508 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.4668 (mpt) REVERT: B 101 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8832 (p) REVERT: B 449 MET cc_start: 0.8887 (tpp) cc_final: 0.8329 (tpp) REVERT: B 561 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: B 586 ARG cc_start: 0.3580 (mtt-85) cc_final: 0.3158 (mtp85) REVERT: C 143 TYR cc_start: 0.8858 (m-80) cc_final: 0.8138 (m-10) REVERT: C 449 MET cc_start: 0.8710 (tpp) cc_final: 0.8052 (tpp) REVERT: C 450 ASP cc_start: 0.8789 (t0) cc_final: 0.8545 (t0) REVERT: D 139 PHE cc_start: 0.9213 (m-80) cc_final: 0.8461 (m-80) REVERT: D 449 MET cc_start: 0.8871 (tpp) cc_final: 0.8215 (tpp) REVERT: D 508 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.4429 (mpt) REVERT: D 561 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: E 63 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8059 (tptp) REVERT: E 139 PHE cc_start: 0.9083 (m-80) cc_final: 0.7846 (m-80) REVERT: E 449 MET cc_start: 0.8928 (tpp) cc_final: 0.8302 (tpp) REVERT: E 450 ASP cc_start: 0.8830 (t0) cc_final: 0.8615 (t0) REVERT: E 561 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: E 586 ARG cc_start: 0.3701 (mtt-85) cc_final: 0.3241 (mtp85) REVERT: F 143 TYR cc_start: 0.8863 (m-80) cc_final: 0.8108 (m-10) REVERT: F 449 MET cc_start: 0.9033 (tpt) cc_final: 0.8804 (tpp) outliers start: 53 outliers final: 25 residues processed: 231 average time/residue: 0.6202 time to fit residues: 176.3839 Evaluate side-chains 206 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 8.9990 chunk 352 optimal weight: 0.4980 chunk 162 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 400 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 394 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.061710 restraints weight = 76794.806| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.09 r_work: 0.2656 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35156 Z= 0.200 Angle : 0.591 9.691 47556 Z= 0.300 Chirality : 0.046 0.182 5364 Planarity : 0.004 0.061 6234 Dihedral : 7.649 58.257 4986 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.53 % Favored : 95.19 % Rotamer: Outliers : 1.72 % Allowed : 11.39 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.40 (0.14), residues: 4344 helix: 1.32 (0.13), residues: 1860 sheet: -0.25 (0.20), residues: 606 loop : -0.56 (0.16), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 113 TYR 0.010 0.001 TYR C 244 PHE 0.016 0.002 PHE B 506 TRP 0.014 0.002 TRP F 454 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00469 (35154) covalent geometry : angle 0.59105 (47556) hydrogen bonds : bond 0.03766 ( 1412) hydrogen bonds : angle 4.16859 ( 4092) Misc. bond : bond 0.00192 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7486 (t-90) cc_final: 0.7072 (t70) REVERT: A 169 ASP cc_start: 0.3311 (OUTLIER) cc_final: 0.2214 (p0) REVERT: A 508 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.4706 (mpt) REVERT: A 586 ARG cc_start: 0.3339 (mtt-85) cc_final: 0.3042 (mtp85) REVERT: B 101 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8817 (p) REVERT: B 449 MET cc_start: 0.8970 (tpp) cc_final: 0.8372 (tpp) REVERT: B 508 MET cc_start: 0.5852 (mmt) cc_final: 0.5268 (mmt) REVERT: B 561 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: B 586 ARG cc_start: 0.3671 (mtt-85) cc_final: 0.3208 (mtp85) REVERT: C 143 TYR cc_start: 0.8847 (m-80) cc_final: 0.8103 (m-10) REVERT: D 139 PHE cc_start: 0.9217 (m-80) cc_final: 0.8940 (m-80) REVERT: D 508 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.4545 (mpt) REVERT: D 561 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8458 (pt0) REVERT: D 586 ARG cc_start: 0.3505 (mtt-85) cc_final: 0.3210 (mtp85) REVERT: E 63 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8041 (tptp) REVERT: E 139 PHE cc_start: 0.9102 (m-80) cc_final: 0.7902 (m-80) REVERT: E 449 MET cc_start: 0.8948 (tpp) cc_final: 0.8330 (tpp) REVERT: E 561 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8369 (pt0) REVERT: E 586 ARG cc_start: 0.3712 (mtt-85) cc_final: 0.3221 (mtp85) REVERT: F 143 TYR cc_start: 0.8855 (m-80) cc_final: 0.8092 (m-10) REVERT: F 449 MET cc_start: 0.9036 (tpt) cc_final: 0.8791 (tpp) REVERT: F 508 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.4734 (mpt) outliers start: 64 outliers final: 34 residues processed: 237 average time/residue: 0.5954 time to fit residues: 172.3200 Evaluate side-chains 218 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 163 PHE Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 229 optimal weight: 8.9990 chunk 306 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 429 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.100046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.060586 restraints weight = 77857.184| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.00 r_work: 0.2634 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 35156 Z= 0.284 Angle : 0.645 9.165 47556 Z= 0.327 Chirality : 0.048 0.166 5364 Planarity : 0.005 0.080 6234 Dihedral : 7.853 59.142 4986 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 2.13 % Allowed : 11.74 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.38 (0.14), residues: 4344 helix: 1.33 (0.13), residues: 1836 sheet: -0.15 (0.21), residues: 600 loop : -0.61 (0.16), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 766 TYR 0.014 0.002 TYR F 138 PHE 0.026 0.002 PHE F 163 TRP 0.013 0.002 TRP F 454 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00660 (35154) covalent geometry : angle 0.64493 (47556) hydrogen bonds : bond 0.04170 ( 1412) hydrogen bonds : angle 4.21500 ( 4092) Misc. bond : bond 0.00292 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 185 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.9011 (mmpt) cc_final: 0.8786 (mmpt) REVERT: A 169 ASP cc_start: 0.3133 (OUTLIER) cc_final: 0.1974 (p0) REVERT: A 449 MET cc_start: 0.8842 (tpp) cc_final: 0.8135 (tpp) REVERT: A 508 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.4766 (mpt) REVERT: A 586 ARG cc_start: 0.3563 (mtt-85) cc_final: 0.3244 (mtp85) REVERT: B 169 ASP cc_start: 0.3218 (OUTLIER) cc_final: 0.2106 (p0) REVERT: B 449 MET cc_start: 0.8944 (tpp) cc_final: 0.8307 (tpp) REVERT: B 561 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8373 (pt0) REVERT: B 586 ARG cc_start: 0.3821 (mtt-85) cc_final: 0.3290 (mtp85) REVERT: C 143 TYR cc_start: 0.8868 (m-80) cc_final: 0.8199 (m-10) REVERT: C 169 ASP cc_start: 0.2826 (OUTLIER) cc_final: 0.1914 (p0) REVERT: C 449 MET cc_start: 0.8953 (tpt) cc_final: 0.8739 (tpp) REVERT: D 169 ASP cc_start: 0.3290 (OUTLIER) cc_final: 0.2265 (p0) REVERT: D 449 MET cc_start: 0.8892 (tpp) cc_final: 0.8309 (tpp) REVERT: D 508 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.4595 (mpt) REVERT: D 561 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8403 (pt0) REVERT: D 586 ARG cc_start: 0.3688 (mtt-85) cc_final: 0.3356 (mtp85) REVERT: E 63 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8103 (tptp) REVERT: E 139 PHE cc_start: 0.9121 (m-80) cc_final: 0.7925 (m-80) REVERT: E 169 ASP cc_start: 0.2998 (OUTLIER) cc_final: 0.1920 (p0) REVERT: E 508 MET cc_start: 0.5928 (mmt) cc_final: 0.5397 (mmt) REVERT: E 561 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: E 586 ARG cc_start: 0.3902 (mtt-85) cc_final: 0.3563 (mtp85) REVERT: F 135 LEU cc_start: 0.9049 (mp) cc_final: 0.8824 (mp) REVERT: F 139 PHE cc_start: 0.9165 (m-10) cc_final: 0.8363 (m-80) REVERT: F 143 TYR cc_start: 0.8920 (m-80) cc_final: 0.8185 (m-10) REVERT: F 169 ASP cc_start: 0.3012 (OUTLIER) cc_final: 0.2409 (p0) REVERT: F 281 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7983 (tp30) REVERT: F 449 MET cc_start: 0.8990 (tpt) cc_final: 0.8781 (tpp) REVERT: F 508 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.4732 (mpt) outliers start: 79 outliers final: 38 residues processed: 252 average time/residue: 0.6092 time to fit residues: 188.2717 Evaluate side-chains 227 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 396 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 430 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 352 optimal weight: 0.2980 chunk 408 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 90 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN F 458 GLN F 602 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.062362 restraints weight = 77168.739| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.07 r_work: 0.2672 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35156 Z= 0.137 Angle : 0.570 10.040 47556 Z= 0.289 Chirality : 0.044 0.260 5364 Planarity : 0.004 0.056 6234 Dihedral : 7.646 58.640 4986 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 1.64 % Allowed : 12.74 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.48 (0.14), residues: 4344 helix: 1.38 (0.13), residues: 1854 sheet: -0.19 (0.21), residues: 582 loop : -0.52 (0.16), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 113 TYR 0.008 0.001 TYR B 134 PHE 0.014 0.001 PHE E 506 TRP 0.015 0.001 TRP F 454 HIS 0.003 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00320 (35154) covalent geometry : angle 0.57021 (47556) hydrogen bonds : bond 0.03458 ( 1412) hydrogen bonds : angle 4.08345 ( 4092) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8737 (mmpt) REVERT: A 158 MET cc_start: 0.8283 (ttp) cc_final: 0.7984 (pp-130) REVERT: A 169 ASP cc_start: 0.3012 (OUTLIER) cc_final: 0.1833 (p0) REVERT: A 586 ARG cc_start: 0.3314 (mtt-85) cc_final: 0.3029 (mtp85) REVERT: B 281 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: B 449 MET cc_start: 0.8939 (tpp) cc_final: 0.8208 (tpp) REVERT: B 561 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: B 586 ARG cc_start: 0.3519 (mtt-85) cc_final: 0.3098 (mtp85) REVERT: C 143 TYR cc_start: 0.8846 (m-80) cc_final: 0.8147 (m-10) REVERT: C 169 ASP cc_start: 0.2511 (OUTLIER) cc_final: 0.1607 (p0) REVERT: C 449 MET cc_start: 0.8957 (tpt) cc_final: 0.8736 (tpp) REVERT: D 117 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8155 (tt) REVERT: D 139 PHE cc_start: 0.9155 (m-80) cc_final: 0.8375 (m-80) REVERT: D 169 ASP cc_start: 0.3106 (OUTLIER) cc_final: 0.2114 (p0) REVERT: D 449 MET cc_start: 0.8927 (tpp) cc_final: 0.8196 (tpp) REVERT: D 508 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.4422 (mpt) REVERT: D 561 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8467 (pt0) REVERT: D 586 ARG cc_start: 0.3416 (mtt-85) cc_final: 0.3137 (mtp85) REVERT: E 63 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8109 (tptp) REVERT: E 139 PHE cc_start: 0.9154 (m-80) cc_final: 0.7943 (m-80) REVERT: E 169 ASP cc_start: 0.2675 (OUTLIER) cc_final: 0.1464 (p0) REVERT: E 442 MET cc_start: 0.9338 (tpp) cc_final: 0.9079 (mpp) REVERT: E 449 MET cc_start: 0.8902 (tpp) cc_final: 0.8346 (tpp) REVERT: E 561 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: E 586 ARG cc_start: 0.3635 (mtt-85) cc_final: 0.3189 (mtp85) REVERT: F 143 TYR cc_start: 0.8868 (m-80) cc_final: 0.8131 (m-10) REVERT: F 169 ASP cc_start: 0.3047 (OUTLIER) cc_final: 0.2467 (p0) REVERT: F 449 MET cc_start: 0.8967 (tpt) cc_final: 0.8744 (tpp) REVERT: F 508 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.4671 (mpt) REVERT: F 568 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8414 (mp-120) outliers start: 61 outliers final: 38 residues processed: 239 average time/residue: 0.5743 time to fit residues: 169.4189 Evaluate side-chains 228 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 568 GLN Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 3 optimal weight: 30.0000 chunk 366 optimal weight: 4.9990 chunk 393 optimal weight: 0.7980 chunk 273 optimal weight: 0.4980 chunk 301 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 305 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 425 optimal weight: 8.9990 chunk 297 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.061099 restraints weight = 76971.013| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.02 r_work: 0.2642 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 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 0.048 35156 Z= 0.224 Angle : 0.620 10.889 47556 Z= 0.312 Chirality : 0.046 0.167 5364 Planarity : 0.004 0.064 6234 Dihedral : 7.733 58.902 4986 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.56 % Favored : 95.30 % Rotamer: Outliers : 1.97 % Allowed : 13.03 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.43 (0.14), residues: 4344 helix: 1.34 (0.13), residues: 1860 sheet: -0.17 (0.21), residues: 594 loop : -0.58 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 766 TYR 0.011 0.002 TYR D 134 PHE 0.018 0.002 PHE E 506 TRP 0.015 0.002 TRP F 454 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00522 (35154) covalent geometry : angle 0.61999 (47556) hydrogen bonds : bond 0.03827 ( 1412) hydrogen bonds : angle 4.10189 ( 4092) Misc. bond : bond 0.00189 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 181 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8975 (mmpt) cc_final: 0.8765 (mmpt) REVERT: A 158 MET cc_start: 0.8273 (ttp) cc_final: 0.7917 (pp-130) REVERT: A 169 ASP cc_start: 0.3059 (OUTLIER) cc_final: 0.1880 (p0) REVERT: A 281 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: A 449 MET cc_start: 0.8830 (tpp) cc_final: 0.8327 (tpp) REVERT: A 586 ARG cc_start: 0.3496 (mtt-85) cc_final: 0.3202 (mtp85) REVERT: B 169 ASP cc_start: 0.3069 (OUTLIER) cc_final: 0.1939 (p0) REVERT: B 281 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: B 449 MET cc_start: 0.8971 (tpp) cc_final: 0.8264 (tpp) REVERT: B 561 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: C 143 TYR cc_start: 0.8851 (m-80) cc_final: 0.8135 (m-10) REVERT: C 169 ASP cc_start: 0.2790 (OUTLIER) cc_final: 0.2214 (p0) REVERT: C 449 MET cc_start: 0.8982 (tpt) cc_final: 0.8763 (tpp) REVERT: D 83 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8106 (mmm-85) REVERT: D 139 PHE cc_start: 0.9134 (m-80) cc_final: 0.8338 (m-80) REVERT: D 169 ASP cc_start: 0.3153 (OUTLIER) cc_final: 0.2140 (p0) REVERT: D 281 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: D 508 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.4543 (mpt) REVERT: D 561 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8445 (pt0) REVERT: D 586 ARG cc_start: 0.3612 (mtt-85) cc_final: 0.3292 (mtp85) REVERT: E 63 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8118 (tptp) REVERT: E 139 PHE cc_start: 0.9152 (m-80) cc_final: 0.7944 (m-80) REVERT: E 169 ASP cc_start: 0.2824 (OUTLIER) cc_final: 0.1708 (p0) REVERT: E 281 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: E 442 MET cc_start: 0.9382 (tpp) cc_final: 0.9111 (mpp) REVERT: E 449 MET cc_start: 0.8990 (tpp) cc_final: 0.8309 (tpp) REVERT: E 508 MET cc_start: 0.5891 (mmt) cc_final: 0.5385 (mmt) REVERT: E 561 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: E 586 ARG cc_start: 0.3690 (mtt-85) cc_final: 0.3185 (mtp85) REVERT: F 83 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8095 (mmm-85) REVERT: F 117 LEU cc_start: 0.8727 (tp) cc_final: 0.8429 (tt) REVERT: F 143 TYR cc_start: 0.8888 (m-80) cc_final: 0.8236 (m-10) REVERT: F 163 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7238 (t80) REVERT: F 169 ASP cc_start: 0.3317 (OUTLIER) cc_final: 0.2721 (p0) REVERT: F 281 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: F 449 MET cc_start: 0.8971 (tpt) cc_final: 0.8739 (tpp) REVERT: F 508 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.4723 (mpt) outliers start: 73 outliers final: 42 residues processed: 244 average time/residue: 0.5975 time to fit residues: 177.6798 Evaluate side-chains 234 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 163 PHE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 306 optimal weight: 10.0000 chunk 375 optimal weight: 20.0000 chunk 201 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 219 optimal weight: 30.0000 chunk 272 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.101105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.061609 restraints weight = 77474.897| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.09 r_work: 0.2650 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35156 Z= 0.176 Angle : 0.612 11.406 47556 Z= 0.307 Chirality : 0.045 0.181 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.678 58.061 4986 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 1.78 % Allowed : 13.41 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.45 (0.14), residues: 4344 helix: 1.40 (0.13), residues: 1854 sheet: -0.20 (0.21), residues: 594 loop : -0.58 (0.16), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 83 TYR 0.013 0.001 TYR A 203 PHE 0.014 0.002 PHE E 506 TRP 0.015 0.002 TRP F 454 HIS 0.003 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00413 (35154) covalent geometry : angle 0.61158 (47556) hydrogen bonds : bond 0.03597 ( 1412) hydrogen bonds : angle 4.06813 ( 4092) Misc. bond : bond 0.00133 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8937 (mmpt) cc_final: 0.8713 (mmpt) REVERT: A 134 TYR cc_start: 0.9065 (m-80) cc_final: 0.8654 (m-10) REVERT: A 158 MET cc_start: 0.8230 (ttp) cc_final: 0.7887 (pp-130) REVERT: A 169 ASP cc_start: 0.2839 (OUTLIER) cc_final: 0.1676 (p0) REVERT: A 281 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: A 449 MET cc_start: 0.8841 (tpp) cc_final: 0.8224 (tpp) REVERT: A 568 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8325 (mp-120) REVERT: A 586 ARG cc_start: 0.3441 (mtt-85) cc_final: 0.3165 (mtp85) REVERT: B 169 ASP cc_start: 0.2891 (OUTLIER) cc_final: 0.1777 (p0) REVERT: B 281 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: B 449 MET cc_start: 0.8952 (tpp) cc_final: 0.8217 (tpp) REVERT: B 561 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8433 (pt0) REVERT: C 117 LEU cc_start: 0.8575 (tp) cc_final: 0.8279 (tt) REVERT: C 143 TYR cc_start: 0.8784 (m-80) cc_final: 0.8144 (m-10) REVERT: C 169 ASP cc_start: 0.2641 (OUTLIER) cc_final: 0.2063 (p0) REVERT: C 449 MET cc_start: 0.8983 (tpt) cc_final: 0.8758 (tpp) REVERT: C 608 MET cc_start: 0.9141 (mtm) cc_final: 0.8936 (mtt) REVERT: D 83 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8189 (mmm-85) REVERT: D 139 PHE cc_start: 0.9143 (m-80) cc_final: 0.8314 (m-80) REVERT: D 169 ASP cc_start: 0.3023 (OUTLIER) cc_final: 0.2024 (p0) REVERT: D 281 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: D 449 MET cc_start: 0.8810 (tpp) cc_final: 0.8444 (tpp) REVERT: D 508 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.4512 (mpt) REVERT: D 561 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8467 (pt0) REVERT: D 568 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8299 (mp-120) REVERT: D 586 ARG cc_start: 0.3557 (mtt-85) cc_final: 0.3262 (mtp85) REVERT: E 63 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8125 (tptp) REVERT: E 139 PHE cc_start: 0.9160 (m-80) cc_final: 0.7909 (m-80) REVERT: E 169 ASP cc_start: 0.2692 (OUTLIER) cc_final: 0.1569 (p0) REVERT: E 281 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: E 442 MET cc_start: 0.9362 (tpp) cc_final: 0.9087 (mpp) REVERT: E 449 MET cc_start: 0.8972 (tpp) cc_final: 0.8253 (tpp) REVERT: E 508 MET cc_start: 0.5823 (mmt) cc_final: 0.5421 (mmt) REVERT: E 561 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: F 83 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8294 (mmm-85) REVERT: F 143 TYR cc_start: 0.8859 (m-80) cc_final: 0.8123 (m-10) REVERT: F 169 ASP cc_start: 0.2993 (OUTLIER) cc_final: 0.2395 (p0) REVERT: F 281 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: F 449 MET cc_start: 0.8957 (tpt) cc_final: 0.8718 (tpp) REVERT: F 508 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.4645 (mpt) outliers start: 66 outliers final: 40 residues processed: 233 average time/residue: 0.6164 time to fit residues: 176.1313 Evaluate side-chains 232 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 357 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 391 optimal weight: 0.9990 chunk 224 optimal weight: 30.0000 chunk 129 optimal weight: 0.3980 chunk 246 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 558 ASN F 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.101914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.062677 restraints weight = 77289.198| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.07 r_work: 0.2679 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35156 Z= 0.134 Angle : 0.586 12.522 47556 Z= 0.293 Chirality : 0.044 0.167 5364 Planarity : 0.004 0.056 6234 Dihedral : 7.544 59.962 4986 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.63 % Rotamer: Outliers : 1.75 % Allowed : 13.57 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.53 (0.14), residues: 4344 helix: 1.50 (0.13), residues: 1854 sheet: -0.23 (0.21), residues: 594 loop : -0.55 (0.16), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 83 TYR 0.009 0.001 TYR D 134 PHE 0.013 0.001 PHE E 152 TRP 0.015 0.001 TRP F 454 HIS 0.004 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00314 (35154) covalent geometry : angle 0.58563 (47556) hydrogen bonds : bond 0.03344 ( 1412) hydrogen bonds : angle 4.00578 ( 4092) Misc. bond : bond 0.00062 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9778.33 seconds wall clock time: 167 minutes 48.60 seconds (10068.60 seconds total)