Starting phenix.real_space_refine on Thu Jul 2 13:53:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i3a_35147/07_2026/8i3a_35147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3a_35147/07_2026/8i3a_35147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i3a_35147/07_2026/8i3a_35147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3a_35147/07_2026/8i3a_35147.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8i3a_35147/07_2026/8i3a_35147.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i3a_35147/07_2026/8i3a_35147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i3a_35147/07_2026/8i3a_35147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3a_35147/07_2026/8i3a_35147.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.140 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5730 2.51 5 N 1476 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8830 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4383 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4383 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.56, per 1000 atoms: 0.18 Number of scatterers: 8830 At special positions: 0 Unit cell: (75.53, 92.13, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1562 8.00 N 1476 7.00 C 5730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 336.2 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 54.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.561A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.834A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 removed outlier: 3.791A pdb=" N LEU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.674A pdb=" N GLN A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 336 through 349 Processing helix chain 'A' and resid 349 through 358 removed outlier: 3.668A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.741A pdb=" N ALA A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.529A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.600A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.504A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.773A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 removed outlier: 3.677A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 removed outlier: 4.061A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 540 removed outlier: 3.562A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 removed outlier: 3.909A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.999A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.377A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 658 removed outlier: 3.884A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 190 removed outlier: 3.561A pdb=" N VAL B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.834A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 removed outlier: 3.791A pdb=" N LEU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.675A pdb=" N GLN B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 336 through 349 Processing helix chain 'B' and resid 349 through 358 removed outlier: 3.667A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.741A pdb=" N ALA B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP B 386 " --> pdb=" O CYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.529A pdb=" N ALA B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 3.600A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.503A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 473 removed outlier: 3.774A pdb=" N ARG B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 485 removed outlier: 3.678A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 removed outlier: 4.061A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 540 removed outlier: 3.562A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 removed outlier: 3.909A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.999A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.377A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.884A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 91 removed outlier: 6.665A pdb=" N ARG A 81 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS A 50 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 83 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG A 48 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER A 85 " --> pdb=" O CYS A 46 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS A 46 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.349A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU A 95 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR A 262 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE A 96 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 279 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 98 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 281 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 100 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 91 removed outlier: 6.664A pdb=" N ARG B 81 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS B 50 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 83 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG B 48 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER B 85 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS B 46 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.348A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU B 95 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR B 262 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 96 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU B 279 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 98 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU B 281 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 100 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 288 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2366 1.33 - 1.45: 1730 1.45 - 1.57: 4826 1.57 - 1.70: 8 1.70 - 1.82: 88 Bond restraints: 9018 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 1.374 1.301 0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C4 ATP A 703 " pdb=" N9 ATP A 703 " ideal model delta sigma weight residual 1.374 1.301 0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.318 0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C5 ATP A 703 " pdb=" N7 ATP A 703 " ideal model delta sigma weight residual 1.387 1.319 0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C4' ATP A 701 " pdb=" O4' ATP A 701 " ideal model delta sigma weight residual 1.444 1.383 0.061 1.10e-02 8.26e+03 3.12e+01 ... (remaining 9013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 12086 3.54 - 7.08: 121 7.08 - 10.62: 23 10.62 - 14.15: 4 14.15 - 17.69: 4 Bond angle restraints: 12238 Sorted by residual: angle pdb=" PB ATP A 703 " pdb=" O3B ATP A 703 " pdb=" PG ATP A 703 " ideal model delta sigma weight residual 139.87 129.18 10.69 1.00e+00 1.00e+00 1.14e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 129.21 10.66 1.00e+00 1.00e+00 1.14e+02 angle pdb=" N3 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 127.04 135.85 -8.81 1.15e+00 7.59e-01 5.89e+01 angle pdb=" N3 ATP A 703 " pdb=" C4 ATP A 703 " pdb=" N9 ATP A 703 " ideal model delta sigma weight residual 127.04 135.85 -8.81 1.15e+00 7.59e-01 5.89e+01 angle pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " ideal model delta sigma weight residual 101.57 113.31 -11.74 1.54e+00 4.24e-01 5.84e+01 ... (remaining 12233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4790 17.35 - 34.70: 418 34.70 - 52.05: 48 52.05 - 69.40: 14 69.40 - 86.75: 6 Dihedral angle restraints: 5276 sinusoidal: 2050 harmonic: 3226 Sorted by residual: dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N TYR B 298 " pdb=" CA TYR B 298 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N TYR A 298 " pdb=" CA TYR A 298 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LEU B 169 " pdb=" C LEU B 169 " pdb=" N PRO B 170 " pdb=" CA PRO B 170 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 5273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1159 0.062 - 0.125: 240 0.125 - 0.187: 50 0.187 - 0.250: 2 0.250 - 0.312: 3 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CB VAL B 566 " pdb=" CA VAL B 566 " pdb=" CG1 VAL B 566 " pdb=" CG2 VAL B 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ASN B 567 " pdb=" N ASN B 567 " pdb=" C ASN B 567 " pdb=" CB ASN B 567 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1451 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 223 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ILE B 223 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE B 223 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 224 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 223 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ILE A 223 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 223 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A 224 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 101 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.74e+00 pdb=" N PRO B 102 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.030 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 33 2.60 - 3.17: 6695 3.17 - 3.75: 13047 3.75 - 4.32: 19569 4.32 - 4.90: 32447 Nonbonded interactions: 71791 Sorted by model distance: nonbonded pdb=" O2' ATP A 701 " pdb=" O3' ATP A 701 " model vdw 2.023 2.432 nonbonded pdb=" O2' ATP A 703 " pdb=" O3' ATP A 703 " model vdw 2.024 2.432 nonbonded pdb=" OH TYR B 152 " pdb=" OE1 GLU B 462 " model vdw 2.356 3.040 nonbonded pdb=" OH TYR A 152 " pdb=" OE1 GLU A 462 " model vdw 2.357 3.040 nonbonded pdb=" OG SER B 108 " pdb="MG MG B 701 " model vdw 2.377 2.170 ... (remaining 71786 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' and resid 32 through 662) selection = (chain 'B' and resid 32 through 662) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 : 0.008 0.096 9018 Z= 0.406 Angle : 1.044 17.692 12238 Z= 0.608 Chirality : 0.056 0.312 1454 Planarity : 0.006 0.054 1488 Dihedral : 13.417 86.745 3200 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.61 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -4.99 (0.17), residues: 1104 helix: -3.22 (0.13), residues: 634 sheet: -1.97 (0.44), residues: 94 loop : -3.47 (0.24), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 587 TYR 0.018 0.002 TYR B 594 PHE 0.022 0.002 PHE B 499 TRP 0.017 0.002 TRP B 447 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.41 ( 9018) covalent geometry : angle 1.04364 / 0.61 (12238) hydrogen bonds : bond 0.18149 / 11.55 ( 390) hydrogen bonds : angle 7.30946 / 5.12 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.318 Fit side-chains REVERT: A 141 ARG cc_start: 0.7547 (mtm180) cc_final: 0.6813 (mmm160) REVERT: A 212 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7705 (ttp80) REVERT: A 285 LYS cc_start: 0.8043 (mttp) cc_final: 0.7723 (mtpt) REVERT: A 462 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7234 (mm-30) REVERT: A 568 LYS cc_start: 0.7914 (tptp) cc_final: 0.7321 (mtpt) REVERT: A 603 MET cc_start: 0.7430 (mtp) cc_final: 0.7103 (mtt) REVERT: B 141 ARG cc_start: 0.7573 (mtm180) cc_final: 0.6874 (mmm160) REVERT: B 212 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7720 (ttp80) REVERT: B 274 MET cc_start: 0.8779 (mtt) cc_final: 0.8529 (mtp) REVERT: B 285 LYS cc_start: 0.8018 (mttp) cc_final: 0.7706 (mtpt) REVERT: B 402 ARG cc_start: 0.7459 (ttm170) cc_final: 0.7206 (ttm170) REVERT: B 462 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7361 (mm-30) REVERT: B 568 LYS cc_start: 0.8535 (mttt) cc_final: 0.8284 (mtpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1219 time to fit residues: 22.1838 Evaluate side-chains 116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN A 254 HIS A 321 ASN A 352 GLN B 112 ASN B 254 HIS B 321 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.140473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.101822 restraints weight = 9137.593| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.89 r_work: 0.2932 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9018 Z= 0.119 Angle : 0.542 6.537 12238 Z= 0.280 Chirality : 0.041 0.143 1454 Planarity : 0.004 0.039 1488 Dihedral : 5.265 25.035 1220 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.02 % Rotamer: Outliers : 0.73 % Allowed : 6.25 % Favored : 93.02 % 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: -3.07 (0.22), residues: 1104 helix: -1.35 (0.18), residues: 628 sheet: -1.95 (0.46), residues: 82 loop : -3.06 (0.25), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 602 TYR 0.012 0.001 TYR B 594 PHE 0.012 0.001 PHE B 42 TRP 0.016 0.001 TRP B 447 HIS 0.005 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9018) covalent geometry : angle 0.54232 / 0.28 (12238) hydrogen bonds : bond 0.03302 / 2.29 ( 390) hydrogen bonds : angle 4.30149 / 3.02 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.326 Fit side-chains REVERT: A 133 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8440 (ptmm) REVERT: A 141 ARG cc_start: 0.8025 (mtm180) cc_final: 0.6832 (mmm160) REVERT: A 193 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8524 (mmmt) REVERT: A 429 ASP cc_start: 0.8263 (t70) cc_final: 0.7911 (t70) REVERT: A 462 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7935 (mm-30) REVERT: A 568 LYS cc_start: 0.8069 (tptp) cc_final: 0.7223 (mtmt) REVERT: B 141 ARG cc_start: 0.8146 (mtm180) cc_final: 0.6983 (mmm160) REVERT: B 285 LYS cc_start: 0.8202 (mttp) cc_final: 0.7918 (mtpt) REVERT: B 402 ARG cc_start: 0.7626 (ttm170) cc_final: 0.7275 (ttm170) REVERT: B 429 ASP cc_start: 0.8229 (t70) cc_final: 0.7882 (t70) REVERT: B 661 LYS cc_start: 0.7196 (mttt) cc_final: 0.6895 (mttm) outliers start: 7 outliers final: 6 residues processed: 127 average time/residue: 0.1194 time to fit residues: 19.4894 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN A 352 GLN A 434 HIS B 352 GLN B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.094004 restraints weight = 9182.197| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.89 r_work: 0.2799 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 9018 Z= 0.306 Angle : 0.692 6.614 12238 Z= 0.347 Chirality : 0.049 0.190 1454 Planarity : 0.004 0.040 1488 Dihedral : 5.528 30.329 1220 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.88 % Favored : 92.93 % Rotamer: Outliers : 2.19 % Allowed : 7.40 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.73 (0.23), residues: 1104 helix: -1.13 (0.19), residues: 642 sheet: -1.72 (0.49), residues: 82 loop : -2.87 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 436 TYR 0.021 0.002 TYR A 594 PHE 0.019 0.002 PHE B 499 TRP 0.018 0.002 TRP A 447 HIS 0.006 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.31 ( 9018) covalent geometry : angle 0.69227 / 0.35 (12238) hydrogen bonds : bond 0.04271 / 2.94 ( 390) hydrogen bonds : angle 4.45560 / 3.13 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.199 Fit side-chains REVERT: A 141 ARG cc_start: 0.8001 (mtm180) cc_final: 0.6863 (mmm160) REVERT: A 237 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.8931 (mt) REVERT: A 285 LYS cc_start: 0.8243 (mttp) cc_final: 0.8027 (mmtt) REVERT: A 397 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8529 (tt) REVERT: A 462 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8040 (mm-30) REVERT: A 568 LYS cc_start: 0.8107 (tptp) cc_final: 0.7241 (mttt) REVERT: B 141 ARG cc_start: 0.8050 (mtm180) cc_final: 0.6910 (mmm160) REVERT: B 237 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.8930 (mt) REVERT: B 285 LYS cc_start: 0.8215 (mttp) cc_final: 0.7928 (mtpt) REVERT: B 431 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8240 (mtt90) REVERT: B 568 LYS cc_start: 0.8472 (mttt) cc_final: 0.7915 (mtmt) outliers start: 21 outliers final: 13 residues processed: 129 average time/residue: 0.1122 time to fit residues: 18.7693 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 431 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.0020 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 265 HIS A 352 GLN A 454 ASN A 531 GLN B 265 HIS B 352 GLN B 454 ASN B 531 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.141033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102408 restraints weight = 9132.601| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.89 r_work: 0.2917 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9018 Z= 0.090 Angle : 0.492 6.825 12238 Z= 0.253 Chirality : 0.039 0.132 1454 Planarity : 0.003 0.036 1488 Dihedral : 4.817 26.667 1220 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.29 % Rotamer: Outliers : 0.83 % Allowed : 9.27 % Favored : 89.90 % 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 (0.24), residues: 1104 helix: -0.12 (0.21), residues: 636 sheet: -1.48 (0.52), residues: 76 loop : -2.65 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 431 TYR 0.008 0.001 TYR A 508 PHE 0.012 0.001 PHE B 42 TRP 0.015 0.001 TRP B 447 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 9018) covalent geometry : angle 0.49182 / 0.25 (12238) hydrogen bonds : bond 0.02542 / 1.78 ( 390) hydrogen bonds : angle 3.77268 / 2.64 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.389 Fit side-chains REVERT: A 141 ARG cc_start: 0.8047 (mtm180) cc_final: 0.6890 (mmm160) REVERT: A 193 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8678 (mmmt) REVERT: A 285 LYS cc_start: 0.8170 (mttp) cc_final: 0.7861 (mmtt) REVERT: A 402 ARG cc_start: 0.7605 (ttm170) cc_final: 0.6879 (mtt-85) REVERT: A 429 ASP cc_start: 0.8308 (t70) cc_final: 0.8079 (t70) REVERT: A 568 LYS cc_start: 0.8177 (tptp) cc_final: 0.7232 (mtpt) REVERT: B 141 ARG cc_start: 0.8066 (mtm180) cc_final: 0.6923 (mmm160) REVERT: B 397 LEU cc_start: 0.8590 (tt) cc_final: 0.8347 (tp) REVERT: B 402 ARG cc_start: 0.7583 (ttm170) cc_final: 0.6881 (mtt-85) REVERT: B 568 LYS cc_start: 0.8431 (mttt) cc_final: 0.7895 (mtpt) outliers start: 8 outliers final: 5 residues processed: 128 average time/residue: 0.1293 time to fit residues: 21.3695 Evaluate side-chains 125 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 265 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 454 ASN B 352 GLN B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.139836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101049 restraints weight = 9138.382| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.90 r_work: 0.2905 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9018 Z= 0.110 Angle : 0.503 6.799 12238 Z= 0.257 Chirality : 0.040 0.142 1454 Planarity : 0.003 0.035 1488 Dihedral : 4.687 26.210 1220 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.02 % Rotamer: Outliers : 1.35 % Allowed : 9.58 % Favored : 89.06 % 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 (0.25), residues: 1104 helix: 0.34 (0.21), residues: 624 sheet: -1.35 (0.53), residues: 76 loop : -2.51 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.010 0.001 TYR A 594 PHE 0.011 0.001 PHE A 42 TRP 0.013 0.001 TRP B 447 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9018) covalent geometry : angle 0.50293 / 0.26 (12238) hydrogen bonds : bond 0.02690 / 1.89 ( 390) hydrogen bonds : angle 3.68763 / 2.58 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.202 Fit side-chains REVERT: A 141 ARG cc_start: 0.8054 (mtm180) cc_final: 0.6910 (mmm160) REVERT: A 193 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8668 (mmmt) REVERT: A 285 LYS cc_start: 0.8186 (mttp) cc_final: 0.7887 (mmtt) REVERT: A 402 ARG cc_start: 0.7596 (ttm170) cc_final: 0.6921 (mtt-85) REVERT: A 429 ASP cc_start: 0.8303 (t70) cc_final: 0.7993 (t70) REVERT: A 568 LYS cc_start: 0.8202 (tptp) cc_final: 0.7265 (mtpt) REVERT: B 141 ARG cc_start: 0.8094 (mtm180) cc_final: 0.6962 (mmm160) REVERT: B 277 THR cc_start: 0.8570 (m) cc_final: 0.8353 (t) REVERT: B 285 LYS cc_start: 0.8178 (mttp) cc_final: 0.7863 (mmtt) REVERT: B 402 ARG cc_start: 0.7578 (ttm170) cc_final: 0.6885 (mtt-85) REVERT: B 420 LEU cc_start: 0.8371 (tp) cc_final: 0.8043 (tp) REVERT: B 568 LYS cc_start: 0.8439 (mttt) cc_final: 0.7915 (mtpt) outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 0.1264 time to fit residues: 21.6239 Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 269 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 454 ASN B 130 ASN B 352 GLN B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.104670 restraints weight = 9082.207| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.98 r_work: 0.2870 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9018 Z= 0.124 Angle : 0.516 6.774 12238 Z= 0.262 Chirality : 0.041 0.146 1454 Planarity : 0.003 0.032 1488 Dihedral : 4.680 26.476 1220 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.71 % Favored : 94.11 % Rotamer: Outliers : 1.46 % Allowed : 10.10 % Favored : 88.44 % 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: -0.95 (0.25), residues: 1104 helix: 0.53 (0.21), residues: 624 sheet: -1.19 (0.55), residues: 76 loop : -2.40 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.011 0.001 TYR A 594 PHE 0.012 0.001 PHE A 499 TRP 0.013 0.001 TRP B 447 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 ( 9018) covalent geometry : angle 0.51593 / 0.26 (12238) hydrogen bonds : bond 0.02787 / 1.94 ( 390) hydrogen bonds : angle 3.68341 / 2.57 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.314 Fit side-chains REVERT: A 141 ARG cc_start: 0.8040 (mtm180) cc_final: 0.6847 (mmm160) REVERT: A 193 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8663 (mmmt) REVERT: A 285 LYS cc_start: 0.8147 (mttp) cc_final: 0.7831 (mmtt) REVERT: A 402 ARG cc_start: 0.7578 (ttm170) cc_final: 0.6925 (mtt-85) REVERT: A 429 ASP cc_start: 0.8298 (t70) cc_final: 0.7911 (t70) REVERT: A 568 LYS cc_start: 0.8189 (tptp) cc_final: 0.7195 (mtpt) REVERT: B 141 ARG cc_start: 0.8068 (mtm180) cc_final: 0.6891 (mmm160) REVERT: B 285 LYS cc_start: 0.8163 (mttp) cc_final: 0.7826 (mmtt) REVERT: B 401 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7599 (mtm180) REVERT: B 402 ARG cc_start: 0.7528 (ttm170) cc_final: 0.6843 (mtt-85) REVERT: B 568 LYS cc_start: 0.8520 (mttt) cc_final: 0.7933 (mtpt) outliers start: 14 outliers final: 11 residues processed: 137 average time/residue: 0.1321 time to fit residues: 23.0287 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 269 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 454 ASN B 352 GLN B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.138581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.098741 restraints weight = 9240.137| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.00 r_work: 0.2839 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9018 Z= 0.136 Angle : 0.529 6.766 12238 Z= 0.267 Chirality : 0.041 0.148 1454 Planarity : 0.003 0.033 1488 Dihedral : 4.704 26.831 1220 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.53 % Favored : 94.29 % Rotamer: Outliers : 1.56 % Allowed : 10.73 % Favored : 87.71 % 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: -0.84 (0.25), residues: 1104 helix: 0.63 (0.21), residues: 622 sheet: -1.08 (0.56), residues: 76 loop : -2.37 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.017 0.001 TYR B 152 PHE 0.012 0.001 PHE B 499 TRP 0.013 0.001 TRP A 447 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9018) covalent geometry : angle 0.52886 / 0.27 (12238) hydrogen bonds : bond 0.02876 / 2.00 ( 390) hydrogen bonds : angle 3.73218 / 2.61 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.325 Fit side-chains REVERT: A 141 ARG cc_start: 0.8014 (mtm180) cc_final: 0.6844 (mmm160) REVERT: A 285 LYS cc_start: 0.8135 (mttp) cc_final: 0.7813 (mmtt) REVERT: A 402 ARG cc_start: 0.7575 (ttm170) cc_final: 0.6932 (mtt-85) REVERT: A 429 ASP cc_start: 0.8273 (t70) cc_final: 0.7851 (t70) REVERT: A 568 LYS cc_start: 0.8193 (tptp) cc_final: 0.7218 (mtmt) REVERT: B 141 ARG cc_start: 0.8043 (mtm180) cc_final: 0.6876 (mmm160) REVERT: B 285 LYS cc_start: 0.8154 (mttp) cc_final: 0.7813 (mmtt) REVERT: B 402 ARG cc_start: 0.7509 (ttm170) cc_final: 0.6832 (mtt-85) REVERT: B 568 LYS cc_start: 0.8527 (mttt) cc_final: 0.7960 (mtmt) outliers start: 15 outliers final: 14 residues processed: 138 average time/residue: 0.1019 time to fit residues: 18.0548 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 434 HIS A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.137464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098781 restraints weight = 9161.548| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.88 r_work: 0.2865 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9018 Z= 0.153 Angle : 0.544 6.823 12238 Z= 0.275 Chirality : 0.042 0.152 1454 Planarity : 0.003 0.032 1488 Dihedral : 4.787 27.512 1220 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 1.77 % Allowed : 10.42 % Favored : 87.81 % 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: -0.95 (0.25), residues: 1104 helix: 0.52 (0.21), residues: 636 sheet: -0.95 (0.57), residues: 76 loop : -2.52 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.018 0.001 TYR B 152 PHE 0.013 0.001 PHE B 499 TRP 0.013 0.001 TRP A 447 HIS 0.005 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 ( 9018) covalent geometry : angle 0.54446 / 0.28 (12238) hydrogen bonds : bond 0.03008 / 2.09 ( 390) hydrogen bonds : angle 3.78515 / 2.65 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.225 Fit side-chains REVERT: A 141 ARG cc_start: 0.8051 (mtm180) cc_final: 0.6920 (mmm160) REVERT: A 285 LYS cc_start: 0.8190 (mttp) cc_final: 0.7879 (mmtt) REVERT: A 402 ARG cc_start: 0.7623 (ttm170) cc_final: 0.6984 (mtt-85) REVERT: A 568 LYS cc_start: 0.8228 (tptp) cc_final: 0.7276 (mtmt) REVERT: B 141 ARG cc_start: 0.8083 (mtm180) cc_final: 0.6954 (mmm160) REVERT: B 285 LYS cc_start: 0.8218 (mttp) cc_final: 0.7947 (mtpt) REVERT: B 402 ARG cc_start: 0.7523 (ttm170) cc_final: 0.6846 (mtt-85) REVERT: B 568 LYS cc_start: 0.8550 (mttt) cc_final: 0.7996 (mtmt) outliers start: 17 outliers final: 17 residues processed: 137 average time/residue: 0.1059 time to fit residues: 18.6991 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 420 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 0.0370 chunk 46 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 454 ASN A 662 HIS B 352 GLN B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.139347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100716 restraints weight = 9170.331| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.93 r_work: 0.2854 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9018 Z= 0.225 Angle : 0.611 6.824 12238 Z= 0.306 Chirality : 0.045 0.169 1454 Planarity : 0.004 0.033 1488 Dihedral : 5.043 29.588 1220 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 1.77 % Allowed : 10.83 % Favored : 87.40 % 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: -1.25 (0.25), residues: 1104 helix: 0.16 (0.21), residues: 640 sheet: -0.94 (0.56), residues: 80 loop : -2.48 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 401 TYR 0.022 0.002 TYR B 152 PHE 0.016 0.002 PHE B 499 TRP 0.013 0.002 TRP A 447 HIS 0.005 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 ( 9018) covalent geometry : angle 0.61135 / 0.31 (12238) hydrogen bonds : bond 0.03497 / 2.41 ( 390) hydrogen bonds : angle 4.01257 / 2.81 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.291 Fit side-chains REVERT: A 36 PHE cc_start: 0.7273 (t80) cc_final: 0.7048 (t80) REVERT: A 141 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7068 (mmm160) REVERT: A 285 LYS cc_start: 0.8215 (mttp) cc_final: 0.7952 (mtpt) REVERT: A 397 LEU cc_start: 0.8765 (tt) cc_final: 0.8548 (tp) REVERT: A 402 ARG cc_start: 0.7621 (ttm170) cc_final: 0.6929 (mtt-85) REVERT: A 429 ASP cc_start: 0.8323 (t70) cc_final: 0.7866 (t70) REVERT: A 568 LYS cc_start: 0.8197 (tptp) cc_final: 0.7262 (mtmt) REVERT: B 36 PHE cc_start: 0.7346 (t80) cc_final: 0.7118 (t80) REVERT: B 141 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7065 (mmm160) REVERT: B 285 LYS cc_start: 0.8222 (mttp) cc_final: 0.7946 (mtpt) REVERT: B 568 LYS cc_start: 0.8545 (mttt) cc_final: 0.7938 (mtpt) outliers start: 17 outliers final: 17 residues processed: 141 average time/residue: 0.1147 time to fit residues: 20.6687 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.0030 chunk 8 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 454 ASN B 352 GLN B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.140596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.102045 restraints weight = 9129.048| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.90 r_work: 0.2909 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9018 Z= 0.093 Angle : 0.493 6.871 12238 Z= 0.251 Chirality : 0.040 0.142 1454 Planarity : 0.003 0.032 1488 Dihedral : 4.561 26.394 1220 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer: Outliers : 1.77 % Allowed : 10.94 % Favored : 87.29 % 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: -0.54 (0.26), residues: 1104 helix: 0.90 (0.22), residues: 628 sheet: -0.84 (0.56), residues: 80 loop : -2.35 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.017 0.001 TYR B 152 PHE 0.010 0.001 PHE A 499 TRP 0.015 0.001 TRP B 447 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 9018) covalent geometry : angle 0.49300 / 0.25 (12238) hydrogen bonds : bond 0.02488 / 1.74 ( 390) hydrogen bonds : angle 3.61296 / 2.52 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.346 Fit side-chains REVERT: A 141 ARG cc_start: 0.8030 (mtm180) cc_final: 0.6911 (mmm160) REVERT: A 285 LYS cc_start: 0.8170 (mttp) cc_final: 0.7868 (mttt) REVERT: A 397 LEU cc_start: 0.8639 (tt) cc_final: 0.8417 (tp) REVERT: A 401 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7409 (ptp-170) REVERT: A 402 ARG cc_start: 0.7657 (ttm170) cc_final: 0.7080 (mtt-85) REVERT: A 429 ASP cc_start: 0.8299 (t70) cc_final: 0.7853 (t70) REVERT: A 568 LYS cc_start: 0.8180 (tptp) cc_final: 0.7265 (mtmt) REVERT: B 141 ARG cc_start: 0.8098 (mtm180) cc_final: 0.6950 (mmm160) REVERT: B 285 LYS cc_start: 0.8152 (mttp) cc_final: 0.7845 (mttt) REVERT: B 401 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7418 (ptp-170) REVERT: B 402 ARG cc_start: 0.7613 (ttm170) cc_final: 0.6980 (mtt-85) REVERT: B 568 LYS cc_start: 0.8595 (mttt) cc_final: 0.8023 (mtpt) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.1230 time to fit residues: 21.0523 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 70 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 454 ASN B 352 GLN B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.137931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099312 restraints weight = 9031.408| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.88 r_work: 0.3022 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9018 Z= 0.116 Angle : 0.512 6.826 12238 Z= 0.259 Chirality : 0.041 0.143 1454 Planarity : 0.003 0.034 1488 Dihedral : 4.555 26.280 1220 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 1.67 % Allowed : 10.94 % Favored : 87.40 % 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: -0.42 (0.26), residues: 1104 helix: 1.00 (0.22), residues: 624 sheet: -0.74 (0.57), residues: 80 loop : -2.29 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 401 TYR 0.019 0.001 TYR B 152 PHE 0.012 0.001 PHE B 499 TRP 0.015 0.001 TRP B 447 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9018) covalent geometry : angle 0.51207 / 0.26 (12238) hydrogen bonds : bond 0.02687 / 1.87 ( 390) hydrogen bonds : angle 3.63203 / 2.53 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.81 seconds wall clock time: 35 minutes 27.03 seconds (2127.03 seconds total)