Starting phenix.real_space_refine on Fri Jul 3 08:11:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8io7_35610/07_2026/8io7_35610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io7_35610/07_2026/8io7_35610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8io7_35610/07_2026/8io7_35610.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8io7_35610/07_2026/8io7_35610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8io7_35610/07_2026/8io7_35610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io7_35610/07_2026/8io7_35610.map" model { file = "/net/cci-nas-00/data/ceres_data/8io7_35610/07_2026/8io7_35610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io7_35610/07_2026/8io7_35610.cif" } resolution = 2.62 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= 0.004 sd= 0.047 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 4 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 8166 2.51 5 N 2194 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s 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: 12876 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "B" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.04, per 1000 atoms: 0.24 Number of scatterers: 12876 At special positions: 0 Unit cell: (103.75, 103.75, 115.37, 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 40 16.00 P 4 15.00 Mg 2 11.99 O 2470 8.00 N 2194 7.00 C 8166 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=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 674.0 milliseconds 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 50.9% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.787A pdb=" N GLY A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.682A pdb=" N GLU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.012A pdb=" N PHE A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.503A pdb=" N THR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.732A pdb=" N LYS A 198 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.549A pdb=" N ARG A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 255 through 284 removed outlier: 3.513A pdb=" N GLN A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.822A pdb=" N SER A 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.844A pdb=" N LEU A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.120A pdb=" N ILE A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.094A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.863A pdb=" N HIS A 506 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 526 removed outlier: 3.533A pdb=" N GLU A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.778A pdb=" N GLN A 546 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 557 through 564 removed outlier: 3.924A pdb=" N ASN A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 Processing helix chain 'A' and resid 613 through 624 removed outlier: 3.710A pdb=" N LYS A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 664 Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.626A pdb=" N SER A 679 " --> pdb=" O ASP A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 712 through 718 removed outlier: 4.175A pdb=" N VAL A 716 " --> pdb=" O TYR A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.658A pdb=" N ASN A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.625A pdb=" N ASP A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 801 removed outlier: 3.662A pdb=" N TRP A 801 " --> pdb=" O ASP A 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 86 Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.788A pdb=" N GLY B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 removed outlier: 3.682A pdb=" N GLU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.014A pdb=" N PHE B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.504A pdb=" N THR B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 removed outlier: 3.734A pdb=" N LYS B 198 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.549A pdb=" N ARG B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 255 through 284 removed outlier: 3.512A pdb=" N GLN B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.822A pdb=" N SER B 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.843A pdb=" N LEU B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 378 through 383 removed outlier: 4.120A pdb=" N ILE B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 411 through 426 removed outlier: 4.093A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 478 through 492 Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.862A pdb=" N HIS B 506 " --> pdb=" O SER B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 526 removed outlier: 3.534A pdb=" N GLU B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.778A pdb=" N GLN B 546 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 557 through 564 removed outlier: 3.925A pdb=" N ASN B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 613 through 624 removed outlier: 3.709A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 664 Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.627A pdb=" N SER B 679 " --> pdb=" O ASP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 699 Processing helix chain 'B' and resid 712 through 718 removed outlier: 4.175A pdb=" N VAL B 716 " --> pdb=" O TYR B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.658A pdb=" N ASN B 750 " --> pdb=" O MET B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 764 Processing helix chain 'B' and resid 770 through 792 removed outlier: 3.626A pdb=" N ASP B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.192A pdb=" N ASN A 88 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 92 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLY A 181 " --> pdb=" O ILE A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.192A pdb=" N ASN A 88 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 209 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 176 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 211 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA A 178 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS A 213 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 180 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218 removed outlier: 3.901A pdb=" N ASN A 221 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'A' and resid 406 through 410 removed outlier: 6.147A pdb=" N GLY A 407 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR A 610 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 475 removed outlier: 8.766A pdb=" N VAL A 474 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 432 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY A 496 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU A 538 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP A 498 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER A 540 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER A 500 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY A 574 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 602 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR A 576 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 removed outlier: 5.529A pdb=" N LYS A 452 " --> pdb=" O HIS A 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 625 through 627 removed outlier: 6.248A pdb=" N VAL A 643 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA A 708 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 645 " --> pdb=" O ALA A 708 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.192A pdb=" N ASN B 88 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 92 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLY B 181 " --> pdb=" O ILE B 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.192A pdb=" N ASN B 88 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 174 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU B 209 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 176 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE B 211 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA B 178 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 213 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 180 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 217 through 218 removed outlier: 3.900A pdb=" N ASN B 221 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AB4, first strand: chain 'B' and resid 406 through 410 removed outlier: 6.146A pdb=" N GLY B 407 " --> pdb=" O THR B 610 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N THR B 610 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 475 removed outlier: 8.766A pdb=" N VAL B 474 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 432 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY B 496 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU B 538 " --> pdb=" O GLY B 496 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP B 498 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N SER B 540 " --> pdb=" O TRP B 498 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER B 500 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY B 574 " --> pdb=" O ALA B 600 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE B 602 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B 576 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 452 through 453 removed outlier: 5.529A pdb=" N LYS B 452 " --> pdb=" O HIS B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 625 through 627 removed outlier: 6.248A pdb=" N VAL B 643 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA B 708 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 645 " --> pdb=" O ALA B 708 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1518 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: 2.31 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2222 1.29 - 1.42: 3573 1.42 - 1.55: 7355 1.55 - 1.68: 10 1.68 - 1.81: 70 Bond restraints: 13230 Sorted by residual: bond pdb=" C GLY B 155 " pdb=" O GLY B 155 " ideal model delta sigma weight residual 1.234 1.160 0.073 1.21e-02 6.83e+03 3.67e+01 bond pdb=" C GLY A 155 " pdb=" O GLY A 155 " ideal model delta sigma weight residual 1.235 1.158 0.077 1.35e-02 5.49e+03 3.26e+01 bond pdb=" O1A TPP A 900 " pdb=" PA TPP A 900 " ideal model delta sigma weight residual 1.479 1.519 -0.040 1.00e-02 1.00e+04 1.61e+01 bond pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 1.516 1.474 0.042 1.09e-02 8.42e+03 1.47e+01 bond pdb=" C GLY A 154 " pdb=" O GLY A 154 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.42e-02 4.96e+03 1.46e+01 ... (remaining 13225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 17480 1.64 - 3.29: 429 3.29 - 4.93: 64 4.93 - 6.57: 23 6.57 - 8.22: 4 Bond angle restraints: 18000 Sorted by residual: angle pdb=" O2B TPP A 900 " pdb=" PB TPP A 900 " pdb=" O3A TPP A 900 " ideal model delta sigma weight residual 104.26 110.74 -6.48 1.33e+00 5.64e-01 2.37e+01 angle pdb=" N GLY B 155 " pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 112.50 107.53 4.97 1.16e+00 7.43e-01 1.83e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 109.40 116.30 -6.90 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N LEU A 157 " pdb=" CA LEU A 157 " pdb=" C LEU A 157 " ideal model delta sigma weight residual 109.40 115.96 -6.56 1.63e+00 3.76e-01 1.62e+01 angle pdb=" O1B TPP A 900 " pdb=" PB TPP A 900 " pdb=" O3A TPP A 900 " ideal model delta sigma weight residual 111.16 104.20 6.96 1.82e+00 3.03e-01 1.47e+01 ... (remaining 17995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 7084 17.68 - 35.37: 517 35.37 - 53.05: 99 53.05 - 70.73: 20 70.73 - 88.42: 16 Dihedral angle restraints: 7736 sinusoidal: 3080 harmonic: 4656 Sorted by residual: dihedral pdb=" CA PHE B 143 " pdb=" C PHE B 143 " pdb=" N ALA B 144 " pdb=" CA ALA B 144 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PHE A 143 " pdb=" C PHE A 143 " pdb=" N ALA A 144 " pdb=" CA ALA A 144 " ideal model delta harmonic sigma weight residual -180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY B 301 " pdb=" C GLY B 301 " pdb=" N TRP B 302 " pdb=" CA TRP B 302 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1640 0.064 - 0.129: 236 0.129 - 0.193: 10 0.193 - 0.257: 0 0.257 - 0.322: 2 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA LEU A 157 " pdb=" N LEU A 157 " pdb=" C LEU A 157 " pdb=" CB LEU A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA LEU B 157 " pdb=" N LEU B 157 " pdb=" C LEU B 157 " pdb=" CB LEU B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU B 157 " pdb=" CB LEU B 157 " pdb=" CD1 LEU B 157 " pdb=" CD2 LEU B 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1885 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 156 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" CD GLU B 156 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 156 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 156 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 156 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" CD GLU A 156 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU A 156 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 156 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 558 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C VAL B 558 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 558 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 559 " 0.009 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 110 2.55 - 3.14: 10560 3.14 - 3.72: 21014 3.72 - 4.31: 30896 4.31 - 4.90: 51245 Nonbonded interactions: 113825 Sorted by model distance: nonbonded pdb=" O2B TPP A 900 " pdb="MG MG A 901 " model vdw 1.959 2.170 nonbonded pdb=" O1B TPP B 900 " pdb="MG MG B 901 " model vdw 1.961 2.170 nonbonded pdb=" OD1 ASN B 215 " pdb="MG MG B 901 " model vdw 2.014 2.170 nonbonded pdb=" OD1 ASN A 215 " pdb="MG MG A 901 " model vdw 2.015 2.170 nonbonded pdb=" O2A TPP B 900 " pdb="MG MG B 901 " model vdw 2.055 2.170 ... (remaining 113820 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.840 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 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 : 0.005 0.077 13230 Z= 0.275 Angle : 0.657 8.217 18000 Z= 0.393 Chirality : 0.045 0.322 1888 Planarity : 0.004 0.037 2364 Dihedral : 13.561 88.417 4756 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.55 (0.20), residues: 1608 helix: 1.13 (0.20), residues: 648 sheet: -0.09 (0.38), residues: 198 loop : -0.06 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 717 TYR 0.009 0.001 TYR B 165 PHE 0.010 0.001 PHE A 296 TRP 0.023 0.002 TRP A 302 HIS 0.010 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.28 (13230) covalent geometry : angle 0.65683 / 0.39 (18000) hydrogen bonds : bond 0.18582 / 12.04 ( 550) hydrogen bonds : angle 6.38359 / 4.64 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.542 Fit side-chains REVERT: A 261 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7463 (mtt-85) REVERT: A 751 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8113 (mtp180) REVERT: B 243 GLU cc_start: 0.8106 (tp30) cc_final: 0.7755 (tp30) REVERT: B 509 ASP cc_start: 0.8503 (m-30) cc_final: 0.8248 (m-30) REVERT: B 688 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7562 (mt-10) outliers start: 0 outliers final: 1 residues processed: 126 average time/residue: 0.6824 time to fit residues: 93.0521 Evaluate side-chains 78 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 382 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.069288 restraints weight = 27207.152| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.77 r_work: 0.2906 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13230 Z= 0.200 Angle : 0.565 7.116 18000 Z= 0.305 Chirality : 0.044 0.134 1888 Planarity : 0.004 0.040 2364 Dihedral : 5.007 39.733 1756 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.11 % Allowed : 6.07 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.75 (0.21), residues: 1608 helix: 1.43 (0.20), residues: 656 sheet: -0.25 (0.37), residues: 214 loop : -0.01 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 428 TYR 0.013 0.001 TYR A 744 PHE 0.017 0.001 PHE B 504 TRP 0.015 0.001 TRP A 302 HIS 0.010 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (13230) covalent geometry : angle 0.56526 / 0.31 (18000) hydrogen bonds : bond 0.05078 / 3.32 ( 550) hydrogen bonds : angle 4.81890 / 3.49 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.382 Fit side-chains REVERT: A 195 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8495 (mm110) REVERT: A 437 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 555 ASP cc_start: 0.8540 (t0) cc_final: 0.7952 (t0) REVERT: A 751 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8485 (mtp180) REVERT: B 243 GLU cc_start: 0.8521 (tp30) cc_final: 0.8111 (tp30) REVERT: B 273 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7590 (tp30) REVERT: B 509 ASP cc_start: 0.8959 (m-30) cc_final: 0.8241 (m-30) REVERT: B 535 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8091 (ttp) REVERT: B 555 ASP cc_start: 0.8129 (t0) cc_final: 0.7743 (t0) outliers start: 15 outliers final: 4 residues processed: 98 average time/residue: 0.5640 time to fit residues: 60.4386 Evaluate side-chains 77 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 775 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 0.0980 chunk 125 optimal weight: 0.0870 chunk 137 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 714 HIS B 39 GLN ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.071921 restraints weight = 26876.127| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.71 r_work: 0.2953 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13230 Z= 0.111 Angle : 0.495 9.597 18000 Z= 0.262 Chirality : 0.041 0.130 1888 Planarity : 0.004 0.040 2364 Dihedral : 4.755 41.156 1754 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.81 % Allowed : 8.00 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1608 helix: 1.71 (0.20), residues: 666 sheet: -0.04 (0.38), residues: 212 loop : 0.06 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 428 TYR 0.009 0.001 TYR A 744 PHE 0.010 0.001 PHE A 504 TRP 0.008 0.001 TRP B 454 HIS 0.007 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13230) covalent geometry : angle 0.49506 / 0.26 (18000) hydrogen bonds : bond 0.04023 / 2.63 ( 550) hydrogen bonds : angle 4.49325 / 3.26 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.334 Fit side-chains REVERT: A 195 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8537 (mm110) REVERT: A 481 GLN cc_start: 0.9037 (mm110) cc_final: 0.8546 (mm-40) REVERT: A 509 ASP cc_start: 0.8860 (m-30) cc_final: 0.8566 (m-30) REVERT: A 555 ASP cc_start: 0.8543 (t0) cc_final: 0.8019 (t0) REVERT: A 751 ARG cc_start: 0.8809 (mtm-85) cc_final: 0.8536 (mtp180) REVERT: B 243 GLU cc_start: 0.8558 (tp30) cc_final: 0.8146 (tp30) REVERT: B 273 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7714 (tp30) REVERT: B 509 ASP cc_start: 0.8929 (m-30) cc_final: 0.8183 (m-30) REVERT: B 555 ASP cc_start: 0.8042 (t0) cc_final: 0.7591 (t0) outliers start: 11 outliers final: 2 residues processed: 98 average time/residue: 0.5535 time to fit residues: 59.4285 Evaluate side-chains 86 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 714 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 106 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 506 HIS A 714 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 384 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.070027 restraints weight = 26973.731| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.71 r_work: 0.2916 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13230 Z= 0.182 Angle : 0.502 5.400 18000 Z= 0.268 Chirality : 0.042 0.131 1888 Planarity : 0.004 0.041 2364 Dihedral : 4.709 40.245 1754 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.41 % Allowed : 8.74 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1608 helix: 1.72 (0.20), residues: 664 sheet: -0.05 (0.38), residues: 212 loop : 0.05 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 428 TYR 0.010 0.001 TYR A 744 PHE 0.011 0.001 PHE B 504 TRP 0.008 0.001 TRP A 302 HIS 0.006 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (13230) covalent geometry : angle 0.50169 / 0.27 (18000) hydrogen bonds : bond 0.04206 / 2.73 ( 550) hydrogen bonds : angle 4.42461 / 3.21 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 195 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8521 (mm110) REVERT: A 273 GLU cc_start: 0.7974 (tp30) cc_final: 0.7704 (tp30) REVERT: A 509 ASP cc_start: 0.8799 (m-30) cc_final: 0.8501 (m-30) REVERT: A 555 ASP cc_start: 0.8557 (t0) cc_final: 0.8137 (t0) REVERT: A 751 ARG cc_start: 0.8807 (mtm-85) cc_final: 0.8548 (mtp180) REVERT: B 243 GLU cc_start: 0.8599 (tp30) cc_final: 0.8147 (tp30) REVERT: B 273 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7740 (tp30) REVERT: B 436 ASP cc_start: 0.8210 (t0) cc_final: 0.7986 (t0) REVERT: B 506 HIS cc_start: 0.8679 (m170) cc_final: 0.7728 (m170) REVERT: B 509 ASP cc_start: 0.8953 (m-30) cc_final: 0.8294 (m-30) REVERT: B 555 ASP cc_start: 0.8109 (t0) cc_final: 0.7515 (t0) REVERT: B 618 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7077 (mtm180) outliers start: 19 outliers final: 6 residues processed: 100 average time/residue: 0.5569 time to fit residues: 61.2870 Evaluate side-chains 90 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 138 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN A 384 ASN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.069227 restraints weight = 27162.019| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.71 r_work: 0.2901 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13230 Z= 0.191 Angle : 0.509 7.661 18000 Z= 0.272 Chirality : 0.043 0.131 1888 Planarity : 0.004 0.044 2364 Dihedral : 4.718 39.808 1754 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.56 % Allowed : 9.48 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.98 (0.21), residues: 1608 helix: 1.69 (0.20), residues: 664 sheet: -0.13 (0.38), residues: 214 loop : 0.02 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 428 TYR 0.010 0.001 TYR A 744 PHE 0.012 0.001 PHE B 504 TRP 0.008 0.001 TRP B 302 HIS 0.006 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (13230) covalent geometry : angle 0.50948 / 0.27 (18000) hydrogen bonds : bond 0.04264 / 2.77 ( 550) hydrogen bonds : angle 4.40694 / 3.20 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 273 GLU cc_start: 0.7978 (tp30) cc_final: 0.7723 (tp30) REVERT: A 509 ASP cc_start: 0.8814 (m-30) cc_final: 0.8511 (m-30) REVERT: A 555 ASP cc_start: 0.8529 (t0) cc_final: 0.8104 (t0) REVERT: A 751 ARG cc_start: 0.8807 (mtm-85) cc_final: 0.8509 (mtp180) REVERT: B 184 GLU cc_start: 0.8880 (tt0) cc_final: 0.8678 (tt0) REVERT: B 243 GLU cc_start: 0.8601 (tp30) cc_final: 0.8211 (tp30) REVERT: B 273 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7792 (tp30) REVERT: B 475 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8648 (mm-30) REVERT: B 487 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 509 ASP cc_start: 0.8991 (m-30) cc_final: 0.8353 (m-30) REVERT: B 555 ASP cc_start: 0.8067 (t0) cc_final: 0.7452 (t0) REVERT: B 618 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7115 (mtm180) outliers start: 21 outliers final: 8 residues processed: 107 average time/residue: 0.5845 time to fit residues: 68.2489 Evaluate side-chains 94 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.0040 chunk 115 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 63 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.071819 restraints weight = 26495.539| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.68 r_work: 0.2951 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13230 Z= 0.101 Angle : 0.478 8.203 18000 Z= 0.252 Chirality : 0.041 0.127 1888 Planarity : 0.004 0.042 2364 Dihedral : 4.564 40.252 1754 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.26 % Allowed : 10.22 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1608 helix: 1.78 (0.20), residues: 668 sheet: -0.11 (0.38), residues: 214 loop : 0.09 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 428 TYR 0.010 0.001 TYR A 744 PHE 0.010 0.001 PHE B 504 TRP 0.007 0.001 TRP B 498 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (13230) covalent geometry : angle 0.47762 / 0.25 (18000) hydrogen bonds : bond 0.03630 / 2.37 ( 550) hydrogen bonds : angle 4.27968 / 3.10 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.504 Fit side-chains REVERT: A 273 GLU cc_start: 0.7951 (tp30) cc_final: 0.7718 (tp30) REVERT: A 481 GLN cc_start: 0.9017 (mm110) cc_final: 0.8205 (mt0) REVERT: A 509 ASP cc_start: 0.8800 (m-30) cc_final: 0.8475 (m-30) REVERT: A 555 ASP cc_start: 0.8497 (t0) cc_final: 0.8024 (t0) REVERT: A 751 ARG cc_start: 0.8792 (mtm-85) cc_final: 0.8509 (mtp180) REVERT: B 195 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8461 (mm110) REVERT: B 243 GLU cc_start: 0.8562 (tp30) cc_final: 0.8167 (tp30) REVERT: B 273 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7762 (tp30) REVERT: B 475 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8706 (mm-30) REVERT: B 487 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8128 (mt-10) REVERT: B 509 ASP cc_start: 0.8968 (m-30) cc_final: 0.8327 (m-30) REVERT: B 555 ASP cc_start: 0.7997 (t0) cc_final: 0.7497 (t0) outliers start: 17 outliers final: 9 residues processed: 110 average time/residue: 0.5461 time to fit residues: 66.1576 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 133 optimal weight: 0.0270 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 149 optimal weight: 0.0060 chunk 96 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.9458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071856 restraints weight = 26553.591| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.70 r_work: 0.2953 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13230 Z= 0.115 Angle : 0.481 6.644 18000 Z= 0.253 Chirality : 0.041 0.127 1888 Planarity : 0.004 0.050 2364 Dihedral : 4.480 40.300 1754 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.33 % Allowed : 10.52 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1608 helix: 1.85 (0.20), residues: 668 sheet: -0.11 (0.38), residues: 214 loop : 0.12 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 428 TYR 0.017 0.001 TYR A 489 PHE 0.010 0.001 PHE B 504 TRP 0.009 0.001 TRP A 498 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (13230) covalent geometry : angle 0.48132 / 0.25 (18000) hydrogen bonds : bond 0.03573 / 2.32 ( 550) hydrogen bonds : angle 4.24708 / 3.08 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.504 Fit side-chains REVERT: A 273 GLU cc_start: 0.7971 (tp30) cc_final: 0.7748 (tp30) REVERT: A 481 GLN cc_start: 0.8968 (mm110) cc_final: 0.8237 (mt0) REVERT: A 509 ASP cc_start: 0.8809 (m-30) cc_final: 0.8466 (m-30) REVERT: A 555 ASP cc_start: 0.8506 (t0) cc_final: 0.8036 (t0) REVERT: A 751 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.8509 (mtp180) REVERT: B 195 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8447 (mm110) REVERT: B 243 GLU cc_start: 0.8591 (tp30) cc_final: 0.8176 (tp30) REVERT: B 273 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7776 (tp30) REVERT: B 475 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8502 (mm-30) REVERT: B 487 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 509 ASP cc_start: 0.8966 (m-30) cc_final: 0.8346 (m-30) REVERT: B 555 ASP cc_start: 0.7943 (t0) cc_final: 0.7452 (t0) REVERT: B 618 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7058 (mtm180) REVERT: B 751 ARG cc_start: 0.8791 (mtm-85) cc_final: 0.8567 (mpp80) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.5537 time to fit residues: 65.9071 Evaluate side-chains 99 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 123 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.070430 restraints weight = 26652.944| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.68 r_work: 0.2925 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13230 Z= 0.181 Angle : 0.516 6.192 18000 Z= 0.272 Chirality : 0.042 0.161 1888 Planarity : 0.004 0.042 2364 Dihedral : 4.525 40.152 1754 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.19 % Allowed : 10.81 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.21), residues: 1608 helix: 1.79 (0.20), residues: 668 sheet: -0.14 (0.38), residues: 214 loop : 0.07 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 428 TYR 0.010 0.001 TYR A 744 PHE 0.011 0.001 PHE B 504 TRP 0.008 0.001 TRP B 302 HIS 0.005 0.001 HIS A 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (13230) covalent geometry : angle 0.51591 / 0.27 (18000) hydrogen bonds : bond 0.03888 / 2.52 ( 550) hydrogen bonds : angle 4.27424 / 3.10 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.534 Fit side-chains REVERT: A 273 GLU cc_start: 0.7974 (tp30) cc_final: 0.7751 (tp30) REVERT: A 481 GLN cc_start: 0.9001 (mm110) cc_final: 0.8265 (mt0) REVERT: A 509 ASP cc_start: 0.8819 (m-30) cc_final: 0.8465 (m-30) REVERT: A 555 ASP cc_start: 0.8493 (t0) cc_final: 0.8023 (t0) REVERT: A 751 ARG cc_start: 0.8813 (mtm-85) cc_final: 0.8513 (mtp180) REVERT: A 764 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8034 (mtt) REVERT: B 243 GLU cc_start: 0.8598 (tp30) cc_final: 0.8211 (tp30) REVERT: B 273 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7798 (tp30) REVERT: B 475 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8452 (mm-30) REVERT: B 487 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 509 ASP cc_start: 0.8970 (m-30) cc_final: 0.8618 (m-30) REVERT: B 555 ASP cc_start: 0.7994 (t0) cc_final: 0.7423 (t0) REVERT: B 618 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7068 (mtm180) outliers start: 16 outliers final: 9 residues processed: 99 average time/residue: 0.4898 time to fit residues: 53.5974 Evaluate side-chains 96 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 44 optimal weight: 0.0670 chunk 119 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN A 714 HIS B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.069215 restraints weight = 27128.528| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.70 r_work: 0.2900 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13230 Z= 0.206 Angle : 0.534 7.296 18000 Z= 0.283 Chirality : 0.043 0.172 1888 Planarity : 0.004 0.043 2364 Dihedral : 4.644 39.861 1754 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.33 % Allowed : 10.67 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.96 (0.21), residues: 1608 helix: 1.69 (0.20), residues: 668 sheet: -0.19 (0.38), residues: 214 loop : -0.00 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 428 TYR 0.011 0.001 TYR A 744 PHE 0.011 0.001 PHE B 504 TRP 0.010 0.001 TRP B 302 HIS 0.005 0.001 HIS A 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (13230) covalent geometry : angle 0.53423 / 0.28 (18000) hydrogen bonds : bond 0.04227 / 2.75 ( 550) hydrogen bonds : angle 4.34144 / 3.14 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.526 Fit side-chains REVERT: A 273 GLU cc_start: 0.7983 (tp30) cc_final: 0.7767 (tp30) REVERT: A 481 GLN cc_start: 0.9045 (mm110) cc_final: 0.8253 (mt0) REVERT: A 509 ASP cc_start: 0.8822 (m-30) cc_final: 0.8486 (m-30) REVERT: A 555 ASP cc_start: 0.8483 (t0) cc_final: 0.8037 (t0) REVERT: A 751 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8477 (mtp180) REVERT: B 243 GLU cc_start: 0.8606 (tp30) cc_final: 0.8238 (tp30) REVERT: B 273 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7810 (tp30) REVERT: B 475 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8678 (mm-30) REVERT: B 509 ASP cc_start: 0.8978 (m-30) cc_final: 0.8625 (m-30) REVERT: B 555 ASP cc_start: 0.8029 (t0) cc_final: 0.7454 (t0) REVERT: B 618 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7103 (mtm180) outliers start: 18 outliers final: 9 residues processed: 99 average time/residue: 0.5233 time to fit residues: 57.0214 Evaluate side-chains 91 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070302 restraints weight = 26196.309| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.72 r_work: 0.2876 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13230 Z= 0.137 Angle : 0.513 7.599 18000 Z= 0.271 Chirality : 0.041 0.169 1888 Planarity : 0.004 0.045 2364 Dihedral : 4.574 39.646 1754 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.96 % Allowed : 11.56 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1608 helix: 1.75 (0.20), residues: 668 sheet: -0.18 (0.38), residues: 214 loop : 0.06 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 428 TYR 0.011 0.001 TYR A 744 PHE 0.011 0.001 PHE B 504 TRP 0.008 0.001 TRP B 194 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13230) covalent geometry : angle 0.51311 / 0.27 (18000) hydrogen bonds : bond 0.03823 / 2.49 ( 550) hydrogen bonds : angle 4.26142 / 3.08 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.576 Fit side-chains REVERT: A 273 GLU cc_start: 0.7924 (tp30) cc_final: 0.7717 (tp30) REVERT: A 385 ASP cc_start: 0.8898 (t0) cc_final: 0.8478 (m-30) REVERT: A 481 GLN cc_start: 0.9000 (mm110) cc_final: 0.8227 (mt0) REVERT: A 506 HIS cc_start: 0.8817 (m-70) cc_final: 0.8315 (m170) REVERT: A 509 ASP cc_start: 0.8807 (m-30) cc_final: 0.8528 (m-30) REVERT: A 555 ASP cc_start: 0.8454 (t0) cc_final: 0.7866 (t0) REVERT: A 746 MET cc_start: 0.9126 (tpp) cc_final: 0.8892 (tpp) REVERT: A 751 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.8482 (mtp180) REVERT: B 243 GLU cc_start: 0.8589 (tp30) cc_final: 0.8203 (tp30) REVERT: B 273 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7848 (tp30) REVERT: B 475 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8652 (mm-30) REVERT: B 509 ASP cc_start: 0.8951 (m-30) cc_final: 0.8607 (m-30) REVERT: B 555 ASP cc_start: 0.7988 (t0) cc_final: 0.7431 (t0) REVERT: B 618 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7058 (mtm180) outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.5371 time to fit residues: 56.9177 Evaluate side-chains 96 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 138 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 71 optimal weight: 0.0010 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.070136 restraints weight = 26119.864| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.73 r_work: 0.2872 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13230 Z= 0.150 Angle : 0.512 7.160 18000 Z= 0.271 Chirality : 0.042 0.167 1888 Planarity : 0.004 0.043 2364 Dihedral : 4.564 39.747 1754 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.81 % Allowed : 11.78 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1608 helix: 1.74 (0.20), residues: 668 sheet: -0.18 (0.38), residues: 214 loop : 0.06 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 428 TYR 0.010 0.001 TYR A 489 PHE 0.011 0.001 PHE B 504 TRP 0.007 0.001 TRP B 454 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (13230) covalent geometry : angle 0.51230 / 0.27 (18000) hydrogen bonds : bond 0.03838 / 2.50 ( 550) hydrogen bonds : angle 4.27249 / 3.08 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3083.86 seconds wall clock time: 53 minutes 37.69 seconds (3217.69 seconds total)