Starting phenix.real_space_refine on Thu Aug 6 04:43:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zbu_74009/08_2026/9zbu_74009.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zbu_74009/08_2026/9zbu_74009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zbu_74009/08_2026/9zbu_74009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zbu_74009/08_2026/9zbu_74009.map" model { file = "/net/cci-nas-00/data/ceres_data/9zbu_74009/08_2026/9zbu_74009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zbu_74009/08_2026/9zbu_74009.cif" } resolution = 3.6 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 80 5.49 5 S 40 5.16 5 C 8156 2.51 5 N 2398 2.21 5 O 2547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13223 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 728 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "J" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 683 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 765 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 765 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 543 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "D" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 543 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "E" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "H" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5756 Classifications: {'peptide': 731} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 687} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 10, 'TRANS': 143} Chain: "W" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 484 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "X" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 484 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "Y" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 484 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8304 SG CYS H 445 40.665 90.977 68.660 1.00 77.09 S ATOM 8328 SG CYS H 448 40.884 94.484 67.131 1.00 76.40 S ATOM 8463 SG CYS H 463 43.996 92.812 68.586 1.00 84.25 S ATOM 8489 SG CYS H 466 41.144 94.061 70.833 1.00 85.32 S ATOM 8234 SG CYS H 436 44.614 73.252 61.679 1.00 91.17 S ATOM 8258 SG CYS H 439 41.344 74.521 60.178 1.00 90.45 S ATOM 8570 SG CYS H 476 41.700 74.122 63.963 1.00 91.09 S ATOM 8589 SG CYS H 479 41.417 71.103 61.669 1.00 95.63 S Time building chain proxies: 2.95, per 1000 atoms: 0.22 Number of scatterers: 13223 At special positions: 0 Unit cell: (113.925, 155.155, 150.815, 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) Zn 2 29.99 S 40 16.00 P 80 15.00 O 2547 8.00 N 2398 7.00 C 8156 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: 1.03 Conformation dependent library (CDL) restraints added in 615.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 801 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 448 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 466 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 445 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 463 " pdb=" ZN H 802 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 439 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 479 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 476 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 436 " Number of angles added : 12 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 41.9% alpha, 16.7% beta 24 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.983A pdb=" N SER A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 removed outlier: 4.257A pdb=" N ILE B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 117 through 132 Processing helix chain 'C' and resid 136 through 154 removed outlier: 3.999A pdb=" N SER C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 117 through 132 removed outlier: 3.526A pdb=" N GLY D 132 " --> pdb=" O TRP D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 154 removed outlier: 3.802A pdb=" N SER D 154 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 108 Processing helix chain 'E' and resid 117 through 132 removed outlier: 3.745A pdb=" N LEU E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 Processing helix chain 'H' and resid 74 through 89 Processing helix chain 'H' and resid 91 through 99 removed outlier: 3.709A pdb=" N ALA H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 107 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 128 through 133 Processing helix chain 'H' and resid 135 through 148 Processing helix chain 'H' and resid 152 through 156 removed outlier: 4.370A pdb=" N ALA H 156 " --> pdb=" O ARG H 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 152 through 156' Processing helix chain 'H' and resid 161 through 171 removed outlier: 3.842A pdb=" N LEU H 165 " --> pdb=" O ASN H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 213 Processing helix chain 'H' and resid 229 through 244 removed outlier: 4.089A pdb=" N GLN H 244 " --> pdb=" O ASN H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 257 through 269 removed outlier: 3.822A pdb=" N THR H 261 " --> pdb=" O LEU H 257 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG H 264 " --> pdb=" O GLN H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 295 Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.835A pdb=" N PHE H 308 " --> pdb=" O SER H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 328 removed outlier: 3.830A pdb=" N TYR H 327 " --> pdb=" O ASP H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 349 Processing helix chain 'H' and resid 360 through 369 Processing helix chain 'H' and resid 380 through 384 removed outlier: 3.995A pdb=" N ALA H 384 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 417 removed outlier: 3.629A pdb=" N ALA H 417 " --> pdb=" O GLN H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 499 removed outlier: 3.646A pdb=" N ALA H 499 " --> pdb=" O GLU H 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 516 removed outlier: 3.696A pdb=" N SER H 516 " --> pdb=" O ARG H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 530 Processing helix chain 'H' and resid 539 through 543 Processing helix chain 'H' and resid 569 through 585 removed outlier: 3.656A pdb=" N ARG H 584 " --> pdb=" O GLN H 580 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 603 through 612 Processing helix chain 'H' and resid 613 through 628 removed outlier: 3.599A pdb=" N PHE H 617 " --> pdb=" O GLY H 613 " (cutoff:3.500A) Processing helix chain 'H' and resid 630 through 634 Processing helix chain 'H' and resid 648 through 662 Processing helix chain 'H' and resid 697 through 711 removed outlier: 3.545A pdb=" N LEU H 711 " --> pdb=" O GLY H 707 " (cutoff:3.500A) Processing helix chain 'H' and resid 712 through 715 Processing helix chain 'T' and resid 13 through 26 removed outlier: 6.932A pdb=" N GLN T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR T 22 " --> pdb=" O HIS T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 46 through 57 Processing helix chain 'T' and resid 68 through 72 Processing helix chain 'T' and resid 100 through 105 Processing helix chain 'T' and resid 117 through 132 removed outlier: 3.504A pdb=" N LEU T 121 " --> pdb=" O THR T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 154 Processing helix chain 'W' and resid 13 through 26 removed outlier: 6.747A pdb=" N GLN W 21 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR W 22 " --> pdb=" O HIS W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 29 No H-bonds generated for 'chain 'W' and resid 27 through 29' Processing helix chain 'W' and resid 46 through 62 Processing helix chain 'X' and resid 13 through 26 removed outlier: 7.353A pdb=" N GLN X 21 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N THR X 22 " --> pdb=" O HIS X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 27 through 29 No H-bonds generated for 'chain 'X' and resid 27 through 29' Processing helix chain 'X' and resid 46 through 62 Processing helix chain 'Y' and resid 13 through 27 removed outlier: 6.874A pdb=" N GLN Y 21 " --> pdb=" O VAL Y 17 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR Y 22 " --> pdb=" O HIS Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 61 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 19 removed outlier: 12.406A pdb=" N SER A 8 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N VAL A 36 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR A 10 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ARG A 34 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS A 12 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N GLU A 32 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 14 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A 30 " --> pdb=" O ALA A 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 44 through 55 current: chain 'A' and resid 91 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 91 through 99 current: chain 'B' and resid 25 through 39 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 42 through 55 current: chain 'B' and resid 89 through 98 Processing sheet with id=AA2, first strand: chain 'E' and resid 89 through 90 Processing sheet with id=AA3, first strand: chain 'H' and resid 16 through 19 removed outlier: 4.218A pdb=" N SER H 48 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA H 7 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL H 46 " --> pdb=" O ALA H 7 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLN H 40 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE H 36 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'H' and resid 273 through 276 removed outlier: 5.659A pdb=" N GLN H 247 " --> pdb=" O LEU H 314 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL H 316 " --> pdb=" O GLN H 247 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N ILE H 353 " --> pdb=" O GLY H 315 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE H 317 " --> pdb=" O ILE H 353 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLY H 355 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE H 319 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TRP H 220 " --> pdb=" O LEU H 354 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA H 219 " --> pdb=" O ARG H 373 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU H 375 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU H 221 " --> pdb=" O LEU H 375 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU H 377 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA H 223 " --> pdb=" O LEU H 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 388 through 393 removed outlier: 3.890A pdb=" N THR H 598 " --> pdb=" O LEU H 392 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR H 552 " --> pdb=" O GLU H 593 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL H 595 " --> pdb=" O THR H 552 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL H 554 " --> pdb=" O VAL H 595 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLN H 597 " --> pdb=" O VAL H 554 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU H 556 " --> pdb=" O GLN H 597 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN H 420 " --> pdb=" O VAL H 551 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU H 553 " --> pdb=" O GLN H 420 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL H 421 " --> pdb=" O LEU H 536 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N GLY H 538 " --> pdb=" O VAL H 421 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU H 423 " --> pdb=" O GLY H 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 433 through 436 removed outlier: 3.616A pdb=" N ALA H 433 " --> pdb=" O VAL H 487 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 453 through 455 Processing sheet with id=AA9, first strand: chain 'H' and resid 635 through 643 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 635 through 643 current: chain 'H' and resid 687 through 690 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'T' and resid 3 through 4 removed outlier: 7.056A pdb=" N ASP W 9 " --> pdb=" O ALA W 33 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE W 35 " --> pdb=" O ASP W 9 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL W 11 " --> pdb=" O PHE W 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE W 42 " --> pdb=" O VAL W 34 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL W 45 " --> pdb=" O TYR X 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR X 43 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL X 34 " --> pdb=" O ALA X 41 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR X 43 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL X 32 " --> pdb=" O TYR X 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 3 through 4 removed outlier: 5.035A pdb=" N ASP T 9 " --> pdb=" O VAL T 31 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL T 32 " --> pdb=" O TYR T 43 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR T 43 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL T 34 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL Y 34 " --> pdb=" O ALA Y 41 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR Y 43 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL Y 32 " --> pdb=" O TYR Y 43 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL Y 11 " --> pdb=" O PHE Y 35 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4026 1.34 - 1.45: 2343 1.45 - 1.57: 7109 1.57 - 1.69: 157 1.69 - 1.81: 61 Bond restraints: 13696 Sorted by residual: bond pdb=" C1' DT G 27 " pdb=" N1 DT G 27 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" C1' DC G 1 " pdb=" N1 DC G 1 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.24e+00 bond pdb=" C3' DG G 26 " pdb=" O3' DG G 26 " ideal model delta sigma weight residual 1.435 1.474 -0.039 1.30e-02 5.92e+03 9.11e+00 bond pdb=" C1' DC J 17 " pdb=" N1 DC J 17 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.70e+00 bond pdb=" C3' DC Z 11 " pdb=" C2' DC Z 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.02e+00 ... (remaining 13691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18256 1.26 - 2.53: 496 2.53 - 3.79: 193 3.79 - 5.05: 15 5.05 - 6.32: 5 Bond angle restraints: 18965 Sorted by residual: angle pdb=" C3' DG G 26 " pdb=" O3' DG G 26 " pdb=" P DT G 27 " ideal model delta sigma weight residual 119.70 125.23 -5.53 1.20e+00 6.94e-01 2.12e+01 angle pdb=" N3 DT G 27 " pdb=" C4 DT G 27 " pdb=" O4 DT G 27 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT Z 3 " pdb=" C4 DT Z 3 " pdb=" O4 DT Z 3 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT J 33 " pdb=" C4 DT J 33 " pdb=" O4 DT J 33 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT G 9 " pdb=" C4 DT G 9 " pdb=" O4 DT G 9 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 18960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 7566 34.04 - 68.08: 356 68.08 - 102.11: 15 102.11 - 136.15: 1 136.15 - 170.19: 3 Dihedral angle restraints: 7941 sinusoidal: 3656 harmonic: 4285 Sorted by residual: dihedral pdb=" C4' DT G 27 " pdb=" C3' DT G 27 " pdb=" O3' DT G 27 " pdb=" P DA G 28 " ideal model delta sinusoidal sigma weight residual 220.00 49.81 170.19 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 32 " pdb=" C3' DC J 32 " pdb=" O3' DC J 32 " pdb=" P DT J 33 " ideal model delta sinusoidal sigma weight residual 220.00 52.08 167.92 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DT G 23 " pdb=" C3' DT G 23 " pdb=" O3' DT G 23 " pdb=" P DC G 24 " ideal model delta sinusoidal sigma weight residual 220.00 57.37 162.63 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 7938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1507 0.034 - 0.068: 361 0.068 - 0.102: 98 0.102 - 0.136: 129 0.136 - 0.170: 39 Chirality restraints: 2134 Sorted by residual: chirality pdb=" C3' DC J 17 " pdb=" C4' DC J 17 " pdb=" O3' DC J 17 " pdb=" C2' DC J 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" C3' DC G 17 " pdb=" C4' DC G 17 " pdb=" O3' DC G 17 " pdb=" C2' DC G 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" P DT G 27 " pdb=" OP1 DT G 27 " pdb=" OP2 DT G 27 " pdb=" O5' DT G 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.50 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 2131 not shown) Planarity restraints: 2175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 683 " -0.124 9.50e-02 1.11e+02 5.59e-02 2.13e+00 pdb=" NE ARG H 683 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG H 683 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 683 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 683 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 512 " -0.122 9.50e-02 1.11e+02 5.50e-02 2.04e+00 pdb=" NE ARG H 512 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG H 512 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG H 512 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 512 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU T 119 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" CD GLU T 119 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU T 119 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU T 119 " 0.009 2.00e-02 2.50e+03 ... (remaining 2172 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3013 2.80 - 3.33: 12517 3.33 - 3.85: 21487 3.85 - 4.38: 24458 4.38 - 4.90: 40394 Nonbonded interactions: 101869 Sorted by model distance: nonbonded pdb=" O ALA Y 36 " pdb=" OD1 ASN Y 37 " model vdw 2.278 3.040 nonbonded pdb=" O ASP H 558 " pdb=" OD1 ASP H 558 " model vdw 2.373 3.040 nonbonded pdb=" N GLU B 98 " pdb=" OE1 GLU B 98 " model vdw 2.392 3.120 nonbonded pdb=" O ASP C 94 " pdb=" OD1 ASP C 94 " model vdw 2.409 3.040 nonbonded pdb=" O ALA Y 15 " pdb=" OD1 ASP Y 19 " model vdw 2.446 3.040 ... (remaining 101864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 89 through 153) selection = (chain 'D' and resid 89 through 153) selection = (chain 'E' and resid 89 through 153) } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.490 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13704 Z= 0.263 Angle : 0.556 6.318 18977 Z= 0.390 Chirality : 0.047 0.170 2134 Planarity : 0.004 0.056 2175 Dihedral : 17.102 170.191 5157 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.24), residues: 1463 helix: 2.10 (0.23), residues: 565 sheet: 1.28 (0.36), residues: 249 loop : 0.92 (0.27), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 683 TYR 0.009 0.001 TYR E 92 PHE 0.013 0.001 PHE B 77 TRP 0.014 0.001 TRP C 108 HIS 0.012 0.001 HIS W 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.26 (13696) covalent geometry : angle 0.55507 / 0.39 (18965) hydrogen bonds : bond 0.14579 / 15.41 ( 551) hydrogen bonds : angle 5.36618 / 6.66 ( 1493) metal coordination : bond 0.00154 / 0.16 ( 8) metal coordination : angle 1.47639 / 3.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7525 (tptt) REVERT: H 683 ARG cc_start: 0.7285 (ttp80) cc_final: 0.7030 (ttp80) REVERT: T 7 THR cc_start: 0.6534 (p) cc_final: 0.6268 (p) REVERT: T 43 TYR cc_start: 0.6014 (m-10) cc_final: 0.5809 (m-10) REVERT: T 66 ASP cc_start: 0.5528 (t0) cc_final: 0.5132 (t0) REVERT: T 92 TYR cc_start: 0.8231 (p90) cc_final: 0.8006 (p90) REVERT: T 131 GLU cc_start: 0.8556 (tp30) cc_final: 0.7861 (tm-30) REVERT: W 35 PHE cc_start: 0.5774 (m-80) cc_final: 0.5547 (m-80) REVERT: X 1 MET cc_start: 0.2884 (tmm) cc_final: 0.2425 (tmm) REVERT: Y 49 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7645 (ttm170) REVERT: Y 54 LEU cc_start: 0.8711 (mm) cc_final: 0.8496 (mm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1079 time to fit residues: 26.9986 Evaluate side-chains 127 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN B 64 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS H 203 GLN ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 464 HIS H 547 HIS ** T 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.134887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104121 restraints weight = 41324.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102990 restraints weight = 24715.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.103631 restraints weight = 20350.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104292 restraints weight = 14801.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104184 restraints weight = 12512.286| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13704 Z= 0.208 Angle : 0.653 12.312 18977 Z= 0.345 Chirality : 0.045 0.301 2134 Planarity : 0.005 0.054 2175 Dihedral : 19.843 178.872 2451 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.32 % Allowed : 5.95 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.23), residues: 1463 helix: 1.69 (0.22), residues: 567 sheet: 1.34 (0.35), residues: 245 loop : 0.64 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG H 587 TYR 0.032 0.002 TYR T 74 PHE 0.027 0.002 PHE B 29 TRP 0.011 0.001 TRP H 118 HIS 0.010 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (13696) covalent geometry : angle 0.63265 / 0.34 (18965) hydrogen bonds : bond 0.04615 / 5.03 ( 551) hydrogen bonds : angle 4.38953 / 5.45 ( 1493) metal coordination : bond 0.01019 / 0.86 ( 8) metal coordination : angle 6.39341 / 12.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8059 (tptp) REVERT: H 427 ARG cc_start: 0.8242 (tpt170) cc_final: 0.7822 (tpt170) REVERT: H 467 ASP cc_start: 0.7548 (m-30) cc_final: 0.7320 (m-30) REVERT: H 627 MET cc_start: 0.8154 (tmm) cc_final: 0.7666 (tmm) REVERT: H 683 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7347 (ttp80) REVERT: T 7 THR cc_start: 0.6425 (p) cc_final: 0.6107 (p) REVERT: T 43 TYR cc_start: 0.6035 (m-10) cc_final: 0.5745 (m-10) REVERT: T 59 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8669 (mmmt) REVERT: T 66 ASP cc_start: 0.5581 (t0) cc_final: 0.5343 (t0) REVERT: T 131 GLU cc_start: 0.8960 (tp30) cc_final: 0.8040 (tm-30) REVERT: T 133 LYS cc_start: 0.7409 (mmtm) cc_final: 0.6379 (mmtm) REVERT: W 35 PHE cc_start: 0.6100 (m-80) cc_final: 0.5859 (m-80) REVERT: X 1 MET cc_start: 0.2999 (tmm) cc_final: 0.2510 (tmm) REVERT: Y 54 LEU cc_start: 0.8806 (mm) cc_final: 0.8395 (mm) outliers start: 16 outliers final: 7 residues processed: 153 average time/residue: 0.1037 time to fit residues: 23.2501 Evaluate side-chains 133 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 536 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 94 optimal weight: 0.0770 chunk 106 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 142 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS H 437 HIS ** H 694 GLN ** 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 = 0.4158 r_free = 0.4158 target = 0.134714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.103957 restraints weight = 40785.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102232 restraints weight = 24539.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.103163 restraints weight = 20708.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.103566 restraints weight = 14578.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103386 restraints weight = 13474.922| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13704 Z= 0.142 Angle : 0.556 10.932 18977 Z= 0.300 Chirality : 0.043 0.299 2134 Planarity : 0.005 0.080 2175 Dihedral : 19.900 179.019 2451 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.07 % Allowed : 7.93 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.23), residues: 1463 helix: 1.74 (0.22), residues: 569 sheet: 1.23 (0.34), residues: 272 loop : 0.59 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 587 TYR 0.014 0.001 TYR T 74 PHE 0.020 0.002 PHE B 77 TRP 0.008 0.001 TRP T 128 HIS 0.009 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (13696) covalent geometry : angle 0.54209 / 0.30 (18965) hydrogen bonds : bond 0.03762 / 4.05 ( 551) hydrogen bonds : angle 4.15389 / 5.25 ( 1493) metal coordination : bond 0.00764 / 0.65 ( 8) metal coordination : angle 4.87764 / 10.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 LYS cc_start: 0.8290 (mmtm) cc_final: 0.8031 (tptt) REVERT: D 91 MET cc_start: 0.6592 (tpp) cc_final: 0.6285 (tpp) REVERT: E 91 MET cc_start: 0.7600 (mmm) cc_final: 0.7244 (mmm) REVERT: H 726 ASP cc_start: 0.7892 (t0) cc_final: 0.7687 (t0) REVERT: T 7 THR cc_start: 0.6419 (p) cc_final: 0.6077 (p) REVERT: T 43 TYR cc_start: 0.6145 (m-80) cc_final: 0.5875 (m-10) REVERT: T 59 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8513 (mmmm) REVERT: T 131 GLU cc_start: 0.8935 (tp30) cc_final: 0.8656 (tp30) REVERT: X 1 MET cc_start: 0.2986 (tmm) cc_final: 0.2588 (tmm) outliers start: 13 outliers final: 10 residues processed: 141 average time/residue: 0.0931 time to fit residues: 19.8257 Evaluate side-chains 133 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 52 GLU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN C 137 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN H 112 ASN H 200 ASN H 464 HIS H 465 HIS H 694 GLN ** T 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.131455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.102317 restraints weight = 40748.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.101360 restraints weight = 25766.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.101541 restraints weight = 22463.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.101654 restraints weight = 17636.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.101764 restraints weight = 15943.159| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13704 Z= 0.174 Angle : 0.601 13.673 18977 Z= 0.317 Chirality : 0.043 0.317 2134 Planarity : 0.005 0.050 2175 Dihedral : 20.101 175.965 2451 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.65 % Allowed : 8.67 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.23), residues: 1463 helix: 1.57 (0.22), residues: 570 sheet: 1.07 (0.33), residues: 284 loop : 0.54 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 146 TYR 0.015 0.001 TYR T 43 PHE 0.026 0.002 PHE B 77 TRP 0.010 0.001 TRP E 128 HIS 0.007 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (13696) covalent geometry : angle 0.57972 / 0.32 (18965) hydrogen bonds : bond 0.04113 / 4.35 ( 551) hydrogen bonds : angle 4.11734 / 5.25 ( 1493) metal coordination : bond 0.00977 / 0.83 ( 8) metal coordination : angle 6.37629 / 13.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: C 135 PHE cc_start: 0.6796 (m-10) cc_final: 0.6581 (m-10) REVERT: D 91 MET cc_start: 0.6573 (tpp) cc_final: 0.6181 (tpp) REVERT: H 726 ASP cc_start: 0.8170 (t0) cc_final: 0.7815 (t0) REVERT: T 7 THR cc_start: 0.6803 (p) cc_final: 0.6492 (p) REVERT: T 43 TYR cc_start: 0.5781 (m-80) cc_final: 0.5459 (m-10) REVERT: T 59 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8572 (mmmm) REVERT: T 131 GLU cc_start: 0.9072 (tp30) cc_final: 0.8784 (tm-30) outliers start: 20 outliers final: 15 residues processed: 141 average time/residue: 0.0967 time to fit residues: 20.7102 Evaluate side-chains 133 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 96 GLN C 137 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.130064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101242 restraints weight = 41063.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100481 restraints weight = 25057.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.100747 restraints weight = 19820.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100776 restraints weight = 16050.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100900 restraints weight = 14758.662| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13704 Z= 0.158 Angle : 0.572 13.186 18977 Z= 0.303 Chirality : 0.043 0.318 2134 Planarity : 0.004 0.050 2175 Dihedral : 20.209 175.376 2451 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.73 % Allowed : 10.16 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.23), residues: 1463 helix: 1.59 (0.22), residues: 573 sheet: 0.97 (0.32), residues: 290 loop : 0.54 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 62 TYR 0.010 0.001 TYR T 43 PHE 0.021 0.002 PHE E 101 TRP 0.010 0.001 TRP E 128 HIS 0.008 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (13696) covalent geometry : angle 0.55063 / 0.30 (18965) hydrogen bonds : bond 0.03756 / 4.00 ( 551) hydrogen bonds : angle 4.05508 / 5.17 ( 1493) metal coordination : bond 0.00928 / 0.79 ( 8) metal coordination : angle 6.15681 / 12.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6984 (mm-30) REVERT: C 135 PHE cc_start: 0.6917 (m-10) cc_final: 0.6690 (m-10) REVERT: D 91 MET cc_start: 0.6588 (tpp) cc_final: 0.6209 (tpp) REVERT: E 91 MET cc_start: 0.7938 (mmm) cc_final: 0.7256 (mmm) REVERT: H 726 ASP cc_start: 0.8168 (t0) cc_final: 0.7769 (t0) REVERT: T 7 THR cc_start: 0.6852 (p) cc_final: 0.6549 (p) REVERT: T 43 TYR cc_start: 0.5726 (m-80) cc_final: 0.5372 (m-10) REVERT: T 59 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8572 (mmmm) REVERT: T 131 GLU cc_start: 0.9034 (tp30) cc_final: 0.8771 (tm-30) outliers start: 21 outliers final: 14 residues processed: 143 average time/residue: 0.0834 time to fit residues: 18.0620 Evaluate side-chains 134 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 HIS Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 132 optimal weight: 0.0040 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN C 137 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 HIS ** 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 = 0.4094 r_free = 0.4094 target = 0.129436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101976 restraints weight = 40751.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098841 restraints weight = 28621.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.099381 restraints weight = 23811.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099663 restraints weight = 17103.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099807 restraints weight = 15566.046| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13704 Z= 0.149 Angle : 0.579 12.796 18977 Z= 0.303 Chirality : 0.043 0.322 2134 Planarity : 0.004 0.050 2175 Dihedral : 20.323 175.477 2451 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.15 % Allowed : 10.90 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.23), residues: 1463 helix: 1.58 (0.22), residues: 574 sheet: 0.72 (0.32), residues: 302 loop : 0.55 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 146 TYR 0.010 0.001 TYR T 43 PHE 0.028 0.002 PHE W 35 TRP 0.010 0.001 TRP E 128 HIS 0.007 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (13696) covalent geometry : angle 0.55716 / 0.30 (18965) hydrogen bonds : bond 0.03716 / 3.94 ( 551) hydrogen bonds : angle 4.04014 / 5.23 ( 1493) metal coordination : bond 0.00842 / 0.69 ( 8) metal coordination : angle 6.23499 / 12.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6461 (mm-30) REVERT: B 58 GLU cc_start: 0.8360 (pp20) cc_final: 0.7787 (pp20) REVERT: C 135 PHE cc_start: 0.6944 (m-10) cc_final: 0.6721 (m-10) REVERT: H 726 ASP cc_start: 0.8136 (t0) cc_final: 0.7829 (t0) REVERT: T 7 THR cc_start: 0.6924 (p) cc_final: 0.6609 (p) REVERT: T 43 TYR cc_start: 0.5753 (m-80) cc_final: 0.5384 (m-10) REVERT: T 131 GLU cc_start: 0.9030 (tp30) cc_final: 0.8717 (tm-30) REVERT: W 34 VAL cc_start: 0.7212 (t) cc_final: 0.6629 (m) REVERT: X 1 MET cc_start: 0.3673 (OUTLIER) cc_final: 0.3225 (tmm) REVERT: Y 54 LEU cc_start: 0.8768 (mm) cc_final: 0.8355 (mm) outliers start: 26 outliers final: 21 residues processed: 151 average time/residue: 0.0841 time to fit residues: 19.4809 Evaluate side-chains 144 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 HIS Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 108 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN C 137 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.127225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097955 restraints weight = 40350.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097953 restraints weight = 24721.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098011 restraints weight = 18829.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098513 restraints weight = 15906.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098512 restraints weight = 14540.314| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13704 Z= 0.179 Angle : 0.614 14.214 18977 Z= 0.320 Chirality : 0.043 0.325 2134 Planarity : 0.005 0.051 2175 Dihedral : 20.530 177.612 2451 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.15 % Allowed : 12.22 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.23), residues: 1463 helix: 1.48 (0.22), residues: 574 sheet: 0.46 (0.31), residues: 309 loop : 0.46 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 146 TYR 0.008 0.001 TYR T 43 PHE 0.031 0.002 PHE W 35 TRP 0.010 0.001 TRP H 289 HIS 0.006 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (13696) covalent geometry : angle 0.58920 / 0.32 (18965) hydrogen bonds : bond 0.04078 / 4.31 ( 551) hydrogen bonds : angle 4.13791 / 5.36 ( 1493) metal coordination : bond 0.01079 / 0.87 ( 8) metal coordination : angle 6.89916 / 14.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: C 135 PHE cc_start: 0.7182 (m-10) cc_final: 0.6924 (m-10) REVERT: H 726 ASP cc_start: 0.8328 (t0) cc_final: 0.7929 (t0) REVERT: T 43 TYR cc_start: 0.5792 (m-80) cc_final: 0.5391 (m-10) REVERT: T 131 GLU cc_start: 0.9024 (tp30) cc_final: 0.8678 (tm-30) REVERT: X 1 MET cc_start: 0.4163 (OUTLIER) cc_final: 0.3648 (tmm) outliers start: 26 outliers final: 24 residues processed: 143 average time/residue: 0.0808 time to fit residues: 17.7470 Evaluate side-chains 145 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 HIS Chi-restraints excluded: chain W residue 35 PHE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 9.9990 chunk 111 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 120 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 64 HIS C 137 HIS C 141 GLN H 483 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.128330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092157 restraints weight = 40147.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093762 restraints weight = 19746.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.094811 restraints weight = 13186.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.095309 restraints weight = 10674.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.095816 restraints weight = 9628.449| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 13704 Z= 0.124 Angle : 0.586 13.568 18977 Z= 0.304 Chirality : 0.042 0.325 2134 Planarity : 0.004 0.051 2175 Dihedral : 20.517 177.422 2451 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.98 % Allowed : 12.80 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.23), residues: 1463 helix: 1.64 (0.22), residues: 569 sheet: 0.49 (0.31), residues: 311 loop : 0.49 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 146 TYR 0.010 0.001 TYR T 43 PHE 0.025 0.001 PHE W 35 TRP 0.010 0.001 TRP T 128 HIS 0.006 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (13696) covalent geometry : angle 0.56433 / 0.30 (18965) hydrogen bonds : bond 0.03547 / 3.76 ( 551) hydrogen bonds : angle 4.01822 / 5.27 ( 1493) metal coordination : bond 0.00656 / 0.54 ( 8) metal coordination : angle 6.27191 / 12.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 GLU cc_start: 0.8200 (pp20) cc_final: 0.7633 (pp20) REVERT: C 135 PHE cc_start: 0.6737 (m-10) cc_final: 0.6522 (m-10) REVERT: H 726 ASP cc_start: 0.8218 (t0) cc_final: 0.7940 (t0) REVERT: T 43 TYR cc_start: 0.5787 (m-80) cc_final: 0.5433 (m-10) REVERT: T 131 GLU cc_start: 0.9046 (tp30) cc_final: 0.8728 (tm-30) REVERT: X 1 MET cc_start: 0.3607 (OUTLIER) cc_final: 0.3253 (tmm) outliers start: 24 outliers final: 22 residues processed: 146 average time/residue: 0.0830 time to fit residues: 18.6912 Evaluate side-chains 145 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 52 GLU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 HIS Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 64 HIS E 136 HIS H 636 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.126628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.090330 restraints weight = 40326.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.092076 restraints weight = 19817.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093134 restraints weight = 13353.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.093660 restraints weight = 10756.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.094085 restraints weight = 9669.830| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13704 Z= 0.167 Angle : 0.617 14.040 18977 Z= 0.319 Chirality : 0.043 0.329 2134 Planarity : 0.005 0.052 2175 Dihedral : 20.665 178.975 2451 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.23 % Allowed : 13.21 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.23), residues: 1463 helix: 1.50 (0.22), residues: 573 sheet: 0.47 (0.31), residues: 301 loop : 0.32 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 146 TYR 0.013 0.001 TYR H 578 PHE 0.031 0.002 PHE W 35 TRP 0.060 0.001 TRP C 95 HIS 0.007 0.001 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (13696) covalent geometry : angle 0.59229 / 0.32 (18965) hydrogen bonds : bond 0.04056 / 4.22 ( 551) hydrogen bonds : angle 4.08061 / 5.34 ( 1493) metal coordination : bond 0.00970 / 0.76 ( 8) metal coordination : angle 6.85151 / 14.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 GLU cc_start: 0.8171 (pp20) cc_final: 0.7594 (pp20) REVERT: B 88 SER cc_start: 0.8406 (t) cc_final: 0.8101 (p) REVERT: H 726 ASP cc_start: 0.8270 (t0) cc_final: 0.7912 (t0) REVERT: T 43 TYR cc_start: 0.5800 (m-80) cc_final: 0.5426 (m-10) REVERT: T 131 GLU cc_start: 0.9111 (tp30) cc_final: 0.8711 (tm-30) REVERT: X 1 MET cc_start: 0.3833 (OUTLIER) cc_final: 0.3467 (tmm) outliers start: 27 outliers final: 25 residues processed: 141 average time/residue: 0.0952 time to fit residues: 20.6283 Evaluate side-chains 148 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 52 GLU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 HIS Chi-restraints excluded: chain W residue 35 PHE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 60 GLN B 64 HIS E 136 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.127680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097937 restraints weight = 40304.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096488 restraints weight = 21621.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.096798 restraints weight = 18304.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097121 restraints weight = 14607.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097167 restraints weight = 12743.045| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13704 Z= 0.127 Angle : 0.593 14.404 18977 Z= 0.305 Chirality : 0.043 0.328 2134 Planarity : 0.004 0.052 2175 Dihedral : 20.682 179.203 2451 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.98 % Allowed : 13.13 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.23), residues: 1463 helix: 1.60 (0.22), residues: 570 sheet: 0.45 (0.31), residues: 307 loop : 0.36 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 146 TYR 0.014 0.001 TYR H 578 PHE 0.023 0.001 PHE E 124 TRP 0.040 0.001 TRP C 95 HIS 0.006 0.001 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (13696) covalent geometry : angle 0.57104 / 0.30 (18965) hydrogen bonds : bond 0.03505 / 3.67 ( 551) hydrogen bonds : angle 3.97553 / 5.23 ( 1493) metal coordination : bond 0.00700 / 0.55 ( 8) metal coordination : angle 6.40686 / 13.15 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7061 (tp30) cc_final: 0.6673 (tp30) REVERT: B 58 GLU cc_start: 0.8412 (pp20) cc_final: 0.7841 (pp20) REVERT: H 726 ASP cc_start: 0.8346 (t0) cc_final: 0.7945 (t0) REVERT: T 43 TYR cc_start: 0.5817 (m-80) cc_final: 0.5414 (m-10) REVERT: T 131 GLU cc_start: 0.9073 (tp30) cc_final: 0.8668 (tm-30) REVERT: X 1 MET cc_start: 0.4256 (OUTLIER) cc_final: 0.3698 (tmm) outliers start: 24 outliers final: 22 residues processed: 143 average time/residue: 0.0911 time to fit residues: 20.0565 Evaluate side-chains 149 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 52 GLU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 HIS Chi-restraints excluded: chain W residue 35 PHE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 105 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.128594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.100280 restraints weight = 40670.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.099476 restraints weight = 24791.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099565 restraints weight = 21054.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099676 restraints weight = 16408.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.099794 restraints weight = 14701.197| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13704 Z= 0.120 Angle : 0.578 14.125 18977 Z= 0.299 Chirality : 0.042 0.328 2134 Planarity : 0.004 0.052 2175 Dihedral : 20.664 179.088 2451 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.15 % Allowed : 13.38 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.23), residues: 1463 helix: 1.67 (0.22), residues: 570 sheet: 0.56 (0.32), residues: 303 loop : 0.37 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 146 TYR 0.015 0.001 TYR H 578 PHE 0.027 0.001 PHE E 124 TRP 0.038 0.001 TRP C 95 HIS 0.006 0.001 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (13696) covalent geometry : angle 0.55641 / 0.30 (18965) hydrogen bonds : bond 0.03397 / 3.54 ( 551) hydrogen bonds : angle 3.88358 / 5.13 ( 1493) metal coordination : bond 0.00666 / 0.50 ( 8) metal coordination : angle 6.25860 / 12.92 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.95 seconds wall clock time: 37 minutes 24.70 seconds (2244.70 seconds total)