Starting phenix.real_space_refine on Mon Jul 6 10:24:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rlh_24530/07_2026/7rlh_24530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlh_24530/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rlh_24530/07_2026/7rlh_24530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlh_24530/07_2026/7rlh_24530.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rlh_24530/07_2026/7rlh_24530.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rlh_24530/07_2026/7rlh_24530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rlh_24530/07_2026/7rlh_24530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlh_24530/07_2026/7rlh_24530.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 6.13, per 1000 atoms: 0.18 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: 2.53 Conformation dependent library (CDL) restraints added in 1.5 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: 1.01 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: 6.19 Time building geometry restraints manager: 3.46 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: 19846 16.75 - 33.49: 1422 33.49 - 50.24: 350 50.24 - 66.98: 30 66.98 - 83.73: 54 Dihedral angle restraints: 21702 sinusoidal: 9132 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 21699 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: 0.12 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: 1.940 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.770 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 13.271 83.727 13554 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/Z covalent geometry : bond 0.00373 / 0.17 (35154) covalent geometry : angle 0.61171 / 0.34 (47556) hydrogen bonds : bond 0.16762 / 11.36 ( 1412) hydrogen bonds : angle 6.13869 / 4.36 ( 4092) Misc. bond : bond 0.83333 / 41.53 ( 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 : 1.353 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: 0.8305 time to fit residues: 294.1607 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 : 1.223 ------------------------------------------------------------------------------- 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... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** 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 D 760 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.103637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.064434 restraints weight = 77166.913| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.08 r_work: 0.2735 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1343 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 : 0.632 8.020 47556 Z= 0.322 Chirality : 0.046 0.156 5364 Planarity : 0.005 0.065 6234 Dihedral : 6.763 52.261 4854 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.30 % Favored : 95.42 % Rotamer: Outliers : 1.10 % Allowed : 5.76 % Favored : 93.13 % 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: 0.32 (0.14), residues: 4344 helix: 1.11 (0.13), residues: 1854 sheet: 0.03 (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 0.010 0.002 TYR F 173 PHE 0.032 0.002 PHE E 139 TRP 0.009 0.002 TRP F 454 HIS 0.004 0.001 HIS E 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (35154) covalent geometry : angle 0.63208 / 0.32 (47556) hydrogen bonds : bond 0.04487 / 3.06 ( 1412) hydrogen bonds : angle 4.76047 / 3.41 ( 4092) Misc. bond : bond 0.00077 / 0.04 ( 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 : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7979 (tpt) cc_final: 0.7774 (tpt) REVERT: A 449 MET cc_start: 0.8998 (tpp) cc_final: 0.8780 (tpp) REVERT: A 508 MET cc_start: 0.5796 (OUTLIER) cc_final: 0.4443 (mpt) REVERT: B 135 LEU cc_start: 0.9134 (mp) cc_final: 0.8769 (mp) REVERT: B 146 ILE cc_start: 0.8194 (mp) cc_final: 0.7988 (tp) REVERT: B 561 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: C 84 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7665 (tpt) REVERT: C 143 TYR cc_start: 0.8821 (m-80) cc_final: 0.8003 (m-10) REVERT: D 134 TYR cc_start: 0.8707 (m-80) cc_final: 0.8439 (m-10) REVERT: D 139 PHE cc_start: 0.9231 (m-80) cc_final: 0.8547 (m-80) REVERT: D 449 MET cc_start: 0.9038 (tpp) cc_final: 0.8213 (tpp) REVERT: E 63 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8047 (tptp) REVERT: E 139 PHE cc_start: 0.9017 (m-80) cc_final: 0.7866 (m-80) REVERT: F 84 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7840 (tpt) REVERT: F 143 TYR cc_start: 0.8854 (m-80) cc_final: 0.8030 (m-10) REVERT: F 450 ASP cc_start: 0.8788 (t0) cc_final: 0.8530 (t0) outliers start: 41 outliers final: 11 residues processed: 230 average time/residue: 0.6272 time to fit residues: 176.6880 Evaluate side-chains 188 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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: 0.8980 chunk 53 optimal weight: 8.9990 chunk 375 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 398 optimal weight: 10.0000 chunk 324 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.102749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.063304 restraints weight = 77420.378| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.10 r_work: 0.2704 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1754 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= 0.175 Angle : 0.586 8.749 47556 Z= 0.299 Chirality : 0.045 0.169 5364 Planarity : 0.005 0.062 6234 Dihedral : 6.646 52.241 4854 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.89 % Favored : 95.83 % Rotamer: Outliers : 1.21 % Allowed : 7.43 % Favored : 91.36 % 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: 0.37 (0.14), residues: 4344 helix: 1.17 (0.13), residues: 1860 sheet: -0.12 (0.21), residues: 594 loop : -0.48 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 323 TYR 0.014 0.002 TYR B 134 PHE 0.018 0.002 PHE B 139 TRP 0.015 0.002 TRP F 454 HIS 0.003 0.001 HIS E 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (35154) covalent geometry : angle 0.58555 / 0.30 (47556) hydrogen bonds : bond 0.04046 / 2.77 ( 1412) hydrogen bonds : angle 4.43581 / 3.17 ( 4092) Misc. bond : bond 0.00263 / 0.13 ( 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 243 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8014 (tpt) cc_final: 0.7475 (tmm) REVERT: A 115 HIS cc_start: 0.7488 (t-90) cc_final: 0.7135 (t70) REVERT: A 508 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.4580 (mpt) REVERT: B 449 MET cc_start: 0.8919 (tpp) cc_final: 0.8398 (tpp) REVERT: B 450 ASP cc_start: 0.8789 (t0) cc_final: 0.8586 (t0) REVERT: B 561 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: B 586 ARG cc_start: 0.3595 (mtt-85) cc_final: 0.3255 (mtp85) REVERT: C 143 TYR cc_start: 0.8871 (m-80) cc_final: 0.8061 (m-10) REVERT: D 115 HIS cc_start: 0.7432 (t-90) cc_final: 0.7176 (t70) REVERT: D 139 PHE cc_start: 0.9222 (m-80) cc_final: 0.8545 (m-80) REVERT: D 236 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8973 (mmmm) REVERT: D 449 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8260 (tpp) REVERT: D 508 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.4356 (mpt) REVERT: D 561 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8343 (pt0) REVERT: E 63 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8033 (tptp) REVERT: E 139 PHE cc_start: 0.9007 (m-80) cc_final: 0.7930 (m-80) REVERT: E 449 MET cc_start: 0.8915 (tpp) cc_final: 0.8233 (tpp) REVERT: E 561 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: F 143 TYR cc_start: 0.8846 (m-80) cc_final: 0.8032 (m-10) REVERT: F 449 MET cc_start: 0.8998 (tpt) cc_final: 0.8763 (tpp) REVERT: F 450 ASP cc_start: 0.8798 (t0) cc_final: 0.8588 (t0) REVERT: F 508 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.4560 (mpt) outliers start: 45 outliers final: 19 residues processed: 226 average time/residue: 0.5961 time to fit residues: 165.4346 Evaluate side-chains 206 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 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 580 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 286 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 425 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 405 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 458 GLN F 602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.103789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.064638 restraints weight = 76720.148| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.08 r_work: 0.2744 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35156 Z= 0.111 Angle : 0.543 9.297 47556 Z= 0.276 Chirality : 0.044 0.179 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.502 51.567 4854 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.01 % Favored : 95.72 % Rotamer: Outliers : 1.02 % Allowed : 8.80 % Favored : 90.17 % 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: 0.44 (0.14), residues: 4344 helix: 1.27 (0.13), residues: 1860 sheet: -0.23 (0.20), residues: 594 loop : -0.44 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 113 TYR 0.011 0.001 TYR F 203 PHE 0.024 0.001 PHE B 139 TRP 0.016 0.002 TRP F 454 HIS 0.002 0.000 HIS D 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (35154) covalent geometry : angle 0.54337 / 0.28 (47556) hydrogen bonds : bond 0.03418 / 2.32 ( 1412) hydrogen bonds : angle 4.27315 / 3.05 ( 4092) Misc. bond : bond 0.00043 / 0.02 ( 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 234 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8052 (tpt) cc_final: 0.7727 (tmm) REVERT: A 115 HIS cc_start: 0.7482 (t-90) cc_final: 0.7084 (t70) REVERT: A 449 MET cc_start: 0.8897 (tpp) cc_final: 0.8216 (tpp) REVERT: A 508 MET cc_start: 0.5696 (OUTLIER) cc_final: 0.4496 (mpt) REVERT: B 508 MET cc_start: 0.5843 (mmt) cc_final: 0.5243 (mmt) REVERT: B 561 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: C 139 PHE cc_start: 0.9276 (m-80) cc_final: 0.8132 (m-80) REVERT: C 143 TYR cc_start: 0.8825 (m-80) cc_final: 0.8051 (m-10) REVERT: D 115 HIS cc_start: 0.7449 (t-90) cc_final: 0.7112 (t70) REVERT: D 139 PHE cc_start: 0.9214 (m-80) cc_final: 0.8555 (m-80) REVERT: D 508 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.4343 (mpt) REVERT: D 561 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: E 63 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8031 (tptp) REVERT: E 139 PHE cc_start: 0.9054 (m-80) cc_final: 0.7926 (m-80) REVERT: E 449 MET cc_start: 0.8959 (tpp) cc_final: 0.8258 (tpp) REVERT: E 508 MET cc_start: 0.5920 (mmt) cc_final: 0.5256 (mmt) REVERT: E 561 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8404 (pt0) REVERT: F 143 TYR cc_start: 0.8798 (m-80) cc_final: 0.8026 (m-10) REVERT: F 449 MET cc_start: 0.8989 (tpt) cc_final: 0.8749 (tpp) REVERT: F 508 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.4572 (mpt) outliers start: 38 outliers final: 18 residues processed: 225 average time/residue: 0.5971 time to fit residues: 166.7138 Evaluate side-chains 204 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 580 ASP 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 559 VAL Chi-restraints excluded: chain E residue 561 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 258 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 364 optimal weight: 7.9990 chunk 417 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 356 optimal weight: 0.0970 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS C 406 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.101445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061946 restraints weight = 77332.957| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.10 r_work: 0.2664 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2182 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= 0.220 Angle : 0.599 9.141 47556 Z= 0.303 Chirality : 0.046 0.185 5364 Planarity : 0.005 0.080 6234 Dihedral : 6.562 52.807 4854 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.35 % Favored : 95.37 % Rotamer: Outliers : 1.24 % Allowed : 10.58 % Favored : 88.18 % 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: 1.28 (0.13), residues: 1860 sheet: -0.20 (0.20), residues: 606 loop : -0.54 (0.16), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 766 TYR 0.012 0.002 TYR F 138 PHE 0.018 0.002 PHE B 506 TRP 0.014 0.002 TRP F 454 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (35154) covalent geometry : angle 0.59870 / 0.30 (47556) hydrogen bonds : bond 0.03946 / 2.72 ( 1412) hydrogen bonds : angle 4.24024 / 3.02 ( 4092) Misc. bond : bond 0.00251 / 0.13 ( 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 239 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7420 (t-90) cc_final: 0.7036 (t70) REVERT: A 508 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.4606 (mpt) REVERT: B 101 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8843 (p) REVERT: B 449 MET cc_start: 0.8877 (tpp) cc_final: 0.8424 (tpp) REVERT: B 561 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: B 586 ARG cc_start: 0.3658 (mtt-85) cc_final: 0.3188 (mtp85) REVERT: C 139 PHE cc_start: 0.9208 (m-80) cc_final: 0.8135 (m-80) REVERT: C 143 TYR cc_start: 0.8825 (m-80) cc_final: 0.8060 (m-10) REVERT: D 115 HIS cc_start: 0.7445 (t-90) cc_final: 0.7235 (t70) REVERT: D 134 TYR cc_start: 0.8865 (m-80) cc_final: 0.8620 (m-80) REVERT: D 139 PHE cc_start: 0.9200 (m-80) cc_final: 0.8509 (m-80) REVERT: D 508 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.4513 (mpt) REVERT: D 561 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: D 586 ARG cc_start: 0.3468 (mtt-85) cc_final: 0.3219 (mtp85) REVERT: E 63 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8036 (tptp) REVERT: E 139 PHE cc_start: 0.9072 (m-80) cc_final: 0.7933 (m-80) REVERT: E 449 MET cc_start: 0.8952 (tpp) cc_final: 0.8306 (tpp) REVERT: E 561 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8415 (pt0) REVERT: E 586 ARG cc_start: 0.3778 (mtt-85) cc_final: 0.3417 (mtp85) REVERT: F 143 TYR cc_start: 0.8868 (m-80) cc_final: 0.8095 (m-10) REVERT: F 449 MET cc_start: 0.9031 (tpt) cc_final: 0.8805 (tpp) REVERT: F 508 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.4669 (mpt) outliers start: 46 outliers final: 24 residues processed: 230 average time/residue: 0.5813 time to fit residues: 165.1566 Evaluate side-chains 208 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 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 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 474 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 7.9990 chunk 352 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 400 optimal weight: 10.0000 chunk 125 optimal weight: 0.2980 chunk 394 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.102040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.062622 restraints weight = 76715.149| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.06 r_work: 0.2688 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2309 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= 0.160 Angle : 0.565 8.943 47556 Z= 0.287 Chirality : 0.045 0.216 5364 Planarity : 0.004 0.054 6234 Dihedral : 6.542 52.388 4854 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.91 % Favored : 95.81 % Rotamer: Outliers : 1.53 % Allowed : 11.15 % Favored : 87.32 % 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: 0.44 (0.14), residues: 4344 helix: 1.32 (0.13), residues: 1860 sheet: -0.18 (0.20), residues: 600 loop : -0.53 (0.16), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 113 TYR 0.010 0.001 TYR A 203 PHE 0.013 0.001 PHE B 506 TRP 0.013 0.001 TRP F 454 HIS 0.003 0.001 HIS E 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (35154) covalent geometry : angle 0.56479 / 0.29 (47556) hydrogen bonds : bond 0.03587 / 2.46 ( 1412) hydrogen bonds : angle 4.14013 / 2.94 ( 4092) Misc. bond : bond 0.00144 / 0.07 ( 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 249 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.4662 (mpt) REVERT: B 101 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8801 (p) REVERT: B 449 MET cc_start: 0.8909 (tpp) cc_final: 0.8265 (tpp) REVERT: B 561 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: B 586 ARG cc_start: 0.3604 (mtt-85) cc_final: 0.3169 (mtp85) REVERT: C 143 TYR cc_start: 0.8832 (m-80) cc_final: 0.8136 (m-10) REVERT: D 134 TYR cc_start: 0.8919 (m-80) cc_final: 0.8626 (m-80) REVERT: D 139 PHE cc_start: 0.9211 (m-80) cc_final: 0.8911 (m-80) REVERT: D 508 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.4530 (mpt) REVERT: D 561 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: D 586 ARG cc_start: 0.3311 (mtt-85) cc_final: 0.3048 (mtp85) REVERT: E 63 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8085 (tptp) REVERT: E 139 PHE cc_start: 0.9079 (m-80) cc_final: 0.7855 (m-80) REVERT: E 449 MET cc_start: 0.8916 (tpp) cc_final: 0.8268 (tpp) REVERT: E 561 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: E 586 ARG cc_start: 0.3646 (mtt-85) cc_final: 0.3196 (mtp85) REVERT: F 143 TYR cc_start: 0.8873 (m-80) cc_final: 0.8080 (m-10) REVERT: F 449 MET cc_start: 0.9016 (tpt) cc_final: 0.8794 (tpp) REVERT: F 508 MET cc_start: 0.6236 (OUTLIER) cc_final: 0.4713 (mpt) outliers start: 57 outliers final: 31 residues processed: 240 average time/residue: 0.6130 time to fit residues: 181.5799 Evaluate side-chains 214 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 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 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 153 LEU 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 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 E residue 88 VAL 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 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: 9.9990 chunk 306 optimal weight: 0.0970 chunk 10 optimal weight: 9.9990 chunk 367 optimal weight: 10.0000 chunk 429 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 234 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN ** A 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** 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 = 0.3741 r_free = 0.3741 target = 0.101374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.061981 restraints weight = 77223.093| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.06 r_work: 0.2664 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2443 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= 0.195 Angle : 0.594 10.012 47556 Z= 0.300 Chirality : 0.045 0.209 5364 Planarity : 0.004 0.060 6234 Dihedral : 6.553 52.466 4854 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.33 % Favored : 95.44 % Rotamer: Outliers : 1.59 % Allowed : 11.90 % Favored : 86.51 % 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: 0.49 (0.14), residues: 4344 helix: 1.40 (0.13), residues: 1842 sheet: -0.17 (0.21), residues: 594 loop : -0.52 (0.16), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 113 TYR 0.013 0.002 TYR A 134 PHE 0.016 0.002 PHE B 506 TRP 0.013 0.001 TRP F 454 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (35154) covalent geometry : angle 0.59397 / 0.30 (47556) hydrogen bonds : bond 0.03705 / 2.54 ( 1412) hydrogen bonds : angle 4.12333 / 2.92 ( 4092) Misc. bond : bond 0.00217 / 0.11 ( 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 243 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.3042 (OUTLIER) cc_final: 0.1954 (p0) REVERT: A 508 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.4690 (mpt) REVERT: A 586 ARG cc_start: 0.3350 (mtt-85) cc_final: 0.3056 (mtp85) REVERT: B 101 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8809 (p) REVERT: B 139 PHE cc_start: 0.8995 (m-80) cc_final: 0.8792 (m-80) REVERT: B 449 MET cc_start: 0.8929 (tpp) cc_final: 0.8306 (tpp) REVERT: B 561 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: B 586 ARG cc_start: 0.3665 (mtt-85) cc_final: 0.3217 (mtp85) REVERT: C 143 TYR cc_start: 0.8780 (m-80) cc_final: 0.8049 (m-10) REVERT: C 450 ASP cc_start: 0.8817 (t0) cc_final: 0.8600 (OUTLIER) REVERT: D 134 TYR cc_start: 0.8907 (m-80) cc_final: 0.8518 (m-80) REVERT: D 139 PHE cc_start: 0.9200 (m-80) cc_final: 0.8934 (m-80) REVERT: D 449 MET cc_start: 0.8891 (tpp) cc_final: 0.8152 (tpp) REVERT: D 508 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.4535 (mpt) REVERT: D 561 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: D 586 ARG cc_start: 0.3521 (mtt-85) cc_final: 0.3222 (mtp85) REVERT: E 63 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8103 (tptp) REVERT: E 139 PHE cc_start: 0.9109 (m-80) cc_final: 0.7898 (m-80) REVERT: E 449 MET cc_start: 0.8970 (tpp) cc_final: 0.8357 (tpp) REVERT: E 508 MET cc_start: 0.5804 (mmt) cc_final: 0.5179 (mmt) REVERT: E 561 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8404 (pt0) REVERT: E 586 ARG cc_start: 0.3694 (mtt-85) cc_final: 0.3229 (mtp85) REVERT: F 143 TYR cc_start: 0.8810 (m-80) cc_final: 0.8019 (m-10) REVERT: F 449 MET cc_start: 0.9011 (tpt) cc_final: 0.8782 (tpp) REVERT: F 508 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.4745 (mpt) outliers start: 59 outliers final: 34 residues processed: 233 average time/residue: 0.6573 time to fit residues: 186.4119 Evaluate side-chains 219 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 611 MET 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 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 88 VAL 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 88 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 396 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 430 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 352 optimal weight: 0.0010 chunk 408 optimal weight: 0.7980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN F 90 ASN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.102446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.063423 restraints weight = 76735.558| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.03 r_work: 0.2704 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35156 Z= 0.128 Angle : 0.565 10.235 47556 Z= 0.284 Chirality : 0.044 0.226 5364 Planarity : 0.004 0.056 6234 Dihedral : 6.481 51.867 4854 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.03 % Favored : 95.83 % Rotamer: Outliers : 1.43 % Allowed : 12.60 % Favored : 85.97 % 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: 0.57 (0.14), residues: 4344 helix: 1.49 (0.13), residues: 1836 sheet: -0.17 (0.21), residues: 582 loop : -0.47 (0.16), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 113 TYR 0.009 0.001 TYR F 134 PHE 0.017 0.001 PHE C 742 TRP 0.016 0.001 TRP F 454 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (35154) covalent geometry : angle 0.56532 / 0.28 (47556) hydrogen bonds : bond 0.03350 / 2.28 ( 1412) hydrogen bonds : angle 4.05885 / 2.88 ( 4092) Misc. bond : bond 0.00163 / 0.08 ( 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 237 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8104 (tpt) REVERT: A 134 TYR cc_start: 0.9002 (m-80) cc_final: 0.8618 (m-10) REVERT: A 169 ASP cc_start: 0.3202 (OUTLIER) cc_final: 0.2049 (p0) REVERT: A 449 MET cc_start: 0.8796 (tpp) cc_final: 0.8371 (tpp) REVERT: B 101 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 169 ASP cc_start: 0.2922 (OUTLIER) cc_final: 0.1862 (p0) REVERT: B 449 MET cc_start: 0.8912 (tpp) cc_final: 0.8213 (tpp) REVERT: B 561 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: C 143 TYR cc_start: 0.8864 (m-80) cc_final: 0.8213 (m-10) REVERT: D 134 TYR cc_start: 0.8895 (m-80) cc_final: 0.8508 (m-80) REVERT: D 169 ASP cc_start: 0.3022 (OUTLIER) cc_final: 0.2026 (p0) REVERT: D 449 MET cc_start: 0.8903 (tpp) cc_final: 0.8095 (tpp) REVERT: D 508 MET cc_start: 0.5928 (OUTLIER) cc_final: 0.4388 (mpt) REVERT: D 561 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8390 (pt0) REVERT: D 586 ARG cc_start: 0.3217 (mtt-85) cc_final: 0.2942 (mtp85) REVERT: E 63 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8110 (tptp) REVERT: E 139 PHE cc_start: 0.9127 (m-80) cc_final: 0.7934 (m-80) REVERT: E 449 MET cc_start: 0.8938 (tpp) cc_final: 0.8381 (tpp) REVERT: E 561 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8443 (pt0) REVERT: E 586 ARG cc_start: 0.3521 (mtt-85) cc_final: 0.3087 (mtp85) REVERT: F 143 TYR cc_start: 0.8876 (m-80) cc_final: 0.8169 (m-10) REVERT: F 169 ASP cc_start: 0.2828 (OUTLIER) cc_final: 0.1818 (p0) REVERT: F 449 MET cc_start: 0.8997 (tpt) cc_final: 0.8768 (tpp) REVERT: F 508 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.4718 (mpt) outliers start: 53 outliers final: 34 residues processed: 227 average time/residue: 0.5811 time to fit residues: 164.2911 Evaluate side-chains 216 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET 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 611 MET 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 169 ASP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 474 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 180 THR Chi-restraints excluded: chain C residue 450 ASP 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 88 VAL 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 508 MET 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 88 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 3 optimal weight: 30.0000 chunk 366 optimal weight: 20.0000 chunk 393 optimal weight: 1.9990 chunk 273 optimal weight: 0.0870 chunk 301 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 305 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 425 optimal weight: 8.9990 chunk 297 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.102897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.063693 restraints weight = 76588.952| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.03 r_work: 0.2709 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35156 Z= 0.118 Angle : 0.561 10.999 47556 Z= 0.281 Chirality : 0.044 0.177 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.409 51.678 4854 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.42 % Favored : 95.44 % Rotamer: Outliers : 1.51 % Allowed : 13.06 % Favored : 85.43 % 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: 0.57 (0.14), residues: 4344 helix: 1.48 (0.13), residues: 1854 sheet: -0.16 (0.20), residues: 588 loop : -0.48 (0.16), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.011 0.001 TYR C 244 PHE 0.012 0.001 PHE F 363 TRP 0.016 0.001 TRP C 454 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (35154) covalent geometry : angle 0.56145 / 0.28 (47556) hydrogen bonds : bond 0.03261 / 2.23 ( 1412) hydrogen bonds : angle 4.02864 / 2.85 ( 4092) Misc. bond : bond 0.00055 / 0.03 ( 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 243 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8125 (tpt) REVERT: A 134 TYR cc_start: 0.9016 (m-80) cc_final: 0.8640 (m-10) REVERT: A 169 ASP cc_start: 0.2547 (OUTLIER) cc_final: 0.1431 (p0) REVERT: A 449 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8244 (tpp) REVERT: B 83 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8323 (mmm-85) REVERT: B 101 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8777 (p) REVERT: B 169 ASP cc_start: 0.2313 (OUTLIER) cc_final: 0.1221 (p0) REVERT: B 449 MET cc_start: 0.8892 (tpp) cc_final: 0.8136 (tpp) REVERT: B 561 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8455 (pt0) REVERT: C 143 TYR cc_start: 0.8812 (m-80) cc_final: 0.8169 (m-10) REVERT: D 139 PHE cc_start: 0.9151 (m-80) cc_final: 0.8404 (m-80) REVERT: D 169 ASP cc_start: 0.2658 (OUTLIER) cc_final: 0.1666 (p0) REVERT: D 449 MET cc_start: 0.8931 (tpp) cc_final: 0.8057 (tpp) REVERT: D 508 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.4511 (mpt) REVERT: D 561 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8460 (pt0) REVERT: D 586 ARG cc_start: 0.3268 (mtt-85) cc_final: 0.2982 (mtp85) REVERT: E 63 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8132 (tptp) REVERT: E 139 PHE cc_start: 0.9115 (m-80) cc_final: 0.7906 (m-80) REVERT: E 169 ASP cc_start: 0.2459 (OUTLIER) cc_final: 0.1211 (p0) REVERT: E 449 MET cc_start: 0.8935 (tpp) cc_final: 0.8382 (tpp) REVERT: E 450 ASP cc_start: 0.8768 (t0) cc_final: 0.8555 (t0) REVERT: E 561 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: F 143 TYR cc_start: 0.8830 (m-80) cc_final: 0.8133 (m-10) REVERT: F 169 ASP cc_start: 0.2626 (OUTLIER) cc_final: 0.1606 (p0) REVERT: F 449 MET cc_start: 0.8968 (tpt) cc_final: 0.8736 (tpp) outliers start: 56 outliers final: 33 residues processed: 232 average time/residue: 0.5704 time to fit residues: 163.3839 Evaluate side-chains 219 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 169 ASP 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 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 101 SER Chi-restraints excluded: chain B residue 169 ASP 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 88 VAL 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 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 88 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 474 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 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: 0.0870 chunk 375 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 219 optimal weight: 30.0000 chunk 272 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** 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 = 0.3749 r_free = 0.3749 target = 0.101743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.062241 restraints weight = 77440.027| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.09 r_work: 0.2670 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2683 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= 0.187 Angle : 0.611 11.170 47556 Z= 0.304 Chirality : 0.045 0.175 5364 Planarity : 0.004 0.064 6234 Dihedral : 6.469 52.546 4854 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.63 % Rotamer: Outliers : 1.56 % Allowed : 13.30 % Favored : 85.14 % 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: 0.52 (0.14), residues: 4344 helix: 1.47 (0.13), residues: 1854 sheet: -0.16 (0.20), residues: 600 loop : -0.56 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 766 TYR 0.013 0.001 TYR A 203 PHE 0.024 0.002 PHE B 742 TRP 0.016 0.002 TRP F 454 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (35154) covalent geometry : angle 0.61075 / 0.30 (47556) hydrogen bonds : bond 0.03605 / 2.47 ( 1412) hydrogen bonds : angle 4.04255 / 2.86 ( 4092) Misc. bond : bond 0.00160 / 0.08 ( 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 244 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8134 (tpt) REVERT: A 134 TYR cc_start: 0.9097 (m-80) cc_final: 0.8733 (m-10) REVERT: A 169 ASP cc_start: 0.3001 (OUTLIER) cc_final: 0.1866 (p0) REVERT: A 442 MET cc_start: 0.9469 (tpp) cc_final: 0.9047 (mpp) REVERT: A 449 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8153 (tpp) REVERT: B 101 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8825 (p) REVERT: B 169 ASP cc_start: 0.2558 (OUTLIER) cc_final: 0.1443 (p0) REVERT: B 449 MET cc_start: 0.8954 (tpp) cc_final: 0.8177 (tpp) REVERT: B 561 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: C 143 TYR cc_start: 0.8842 (m-80) cc_final: 0.8187 (m-10) REVERT: D 62 LYS cc_start: 0.9057 (mmpt) cc_final: 0.8761 (mmpt) REVERT: D 83 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8125 (mmm-85) REVERT: D 134 TYR cc_start: 0.8845 (m-80) cc_final: 0.8556 (m-80) REVERT: D 139 PHE cc_start: 0.9106 (m-80) cc_final: 0.8384 (m-80) REVERT: D 169 ASP cc_start: 0.2832 (OUTLIER) cc_final: 0.1835 (p0) REVERT: D 449 MET cc_start: 0.8980 (tpp) cc_final: 0.8036 (tpp) REVERT: D 508 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.4600 (mpt) REVERT: D 561 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: E 63 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8118 (tptp) REVERT: E 83 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8158 (mmm-85) REVERT: E 139 PHE cc_start: 0.9128 (m-80) cc_final: 0.7907 (m-80) REVERT: E 169 ASP cc_start: 0.2498 (OUTLIER) cc_final: 0.1431 (p0) REVERT: E 561 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: F 83 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8274 (mmm-85) REVERT: F 143 TYR cc_start: 0.8884 (m-80) cc_final: 0.8137 (m-10) REVERT: F 169 ASP cc_start: 0.2647 (OUTLIER) cc_final: 0.1663 (p0) REVERT: F 281 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8065 (tp30) REVERT: F 449 MET cc_start: 0.8988 (tpt) cc_final: 0.8750 (tpp) REVERT: F 508 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.4721 (mpt) outliers start: 58 outliers final: 39 residues processed: 232 average time/residue: 0.5563 time to fit residues: 159.4135 Evaluate side-chains 231 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 449 MET 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 101 SER Chi-restraints excluded: chain B residue 169 ASP 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 180 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 550 MET 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 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: 0.0040 chunk 224 optimal weight: 30.0000 chunk 129 optimal weight: 0.0040 chunk 246 optimal weight: 1.9990 overall best weight: 1.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.102078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.062847 restraints weight = 76945.547| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.04 r_work: 0.2688 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2736 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= 0.154 Angle : 0.599 11.452 47556 Z= 0.299 Chirality : 0.044 0.160 5364 Planarity : 0.004 0.054 6234 Dihedral : 6.457 52.346 4854 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.42 % Favored : 95.44 % Rotamer: Outliers : 1.51 % Allowed : 13.35 % Favored : 85.14 % 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: 0.50 (0.14), residues: 4344 helix: 1.46 (0.13), residues: 1854 sheet: -0.20 (0.20), residues: 600 loop : -0.58 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 83 TYR 0.011 0.001 TYR F 138 PHE 0.026 0.001 PHE E 742 TRP 0.011 0.001 TRP C 454 HIS 0.003 0.001 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (35154) covalent geometry : angle 0.59884 / 0.30 (47556) hydrogen bonds : bond 0.03481 / 2.38 ( 1412) hydrogen bonds : angle 4.03319 / 2.85 ( 4092) Misc. bond : bond 0.00112 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9696.11 seconds wall clock time: 166 minutes 26.17 seconds (9986.17 seconds total)