Starting phenix.real_space_refine on Sun Oct 25 02:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m4d_63623/10_2026/9m4d_63623.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m4d_63623/10_2026/9m4d_63623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m4d_63623/10_2026/9m4d_63623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m4d_63623/10_2026/9m4d_63623.map" model { file = "/net/cci-nas-00/data/ceres_data/9m4d_63623/10_2026/9m4d_63623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m4d_63623/10_2026/9m4d_63623.cif" } resolution = 3.15 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= 0.003 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 9576 2.51 5 N 2599 2.21 5 O 2910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15135 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4909 Classifications: {'peptide': 633} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 606} Chain: "B" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4837 Classifications: {'peptide': 623} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "C" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 4945 Classifications: {'peptide': 639} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 612} Chain: "G" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 148 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "H" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 148 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "I" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 148 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Time building chain proxies: 3.20, per 1000 atoms: 0.21 Number of scatterers: 15135 At special positions: 0 Unit cell: (119.14, 167.647, 114.034, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2910 8.00 N 2599 7.00 C 9576 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: 1.17 Conformation dependent library (CDL) restraints added in 727.3 milliseconds 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 23 sheets defined 13.8% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.528A pdb=" N TYR A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.917A pdb=" N LEU A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.555A pdb=" N SER A 499 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.531A pdb=" N MET B 235 " --> pdb=" O PRO B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.565A pdb=" N ASN B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 364 Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.608A pdb=" N GLY B 457 " --> pdb=" O TRP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 removed outlier: 3.988A pdb=" N LEU B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 486 " --> pdb=" O HIS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 294 through 300 removed outlier: 3.831A pdb=" N ASN C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 475 through 493 removed outlier: 4.090A pdb=" N LEU C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 499 removed outlier: 3.675A pdb=" N SER C 499 " --> pdb=" O SER C 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 152 removed outlier: 4.410A pdb=" N ASP G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 147 through 152' Processing helix chain 'G' and resid 153 through 156 Proline residue: G 156 - end of helix No H-bonds generated for 'chain 'G' and resid 153 through 156' Processing helix chain 'G' and resid 157 through 165 removed outlier: 4.081A pdb=" N ILE G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU G 162 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN G 164 " --> pdb=" O THR G 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 165 removed outlier: 3.685A pdb=" N THR H 153 " --> pdb=" O TYR H 149 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA H 155 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Proline residue: H 156 - end of helix removed outlier: 3.807A pdb=" N THR H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU H 162 " --> pdb=" O ALA H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 154 removed outlier: 3.960A pdb=" N VAL I 154 " --> pdb=" O ASP I 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 151 through 154' Processing helix chain 'I' and resid 155 through 164 removed outlier: 3.995A pdb=" N THR I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR I 160 " --> pdb=" O PRO I 156 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE I 161 " --> pdb=" O LEU I 157 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.264A pdb=" N ILE A 336 " --> pdb=" O MET A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 285 removed outlier: 4.076A pdb=" N ALA A 316 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ILE A 353 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS A 315 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TRP A 355 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS A 317 " --> pdb=" O TRP A 355 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N ILE A 357 " --> pdb=" O HIS A 317 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N ARG A 319 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE A 353 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N TYR A 384 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TRP A 355 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL A 386 " --> pdb=" O TRP A 355 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 357 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 407 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG A 383 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP A 427 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.181A pdb=" N TYR A 369 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ASP A 395 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 371 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TYR A 464 " --> pdb=" O ASP A 545 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU A 547 " --> pdb=" O TYR A 464 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ILE A 544 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 571 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N THR A 546 " --> pdb=" O ALA A 571 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N ILE A 573 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N LYS A 548 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ALA A 575 " --> pdb=" O LYS A 548 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASN A 570 " --> pdb=" O GLU A 615 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN A 617 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET A 572 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 619 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU A 574 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE A 621 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 366 through 367 removed outlier: 5.460A pdb=" N VAL A 367 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER A 389 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU A 411 " --> pdb=" O ASP A 460 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 439 removed outlier: 7.495A pdb=" N ASN A 438 " --> pdb=" O ALA A 513 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 Processing sheet with id=AA8, first strand: chain 'A' and resid 632 through 634 removed outlier: 6.381A pdb=" N VAL A 632 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLU B 642 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 634 " --> pdb=" O GLU B 642 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP B 644 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN B 639 " --> pdb=" O ALA C 655 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ARG C 657 " --> pdb=" O GLN B 639 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE B 641 " --> pdb=" O ARG C 657 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TRP C 659 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER B 643 " --> pdb=" O TRP C 659 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE C 672 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA C 655 " --> pdb=" O TYR C 670 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR C 670 " --> pdb=" O ALA C 655 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG C 657 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR C 668 " --> pdb=" O ARG C 657 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TRP C 659 " --> pdb=" O GLN C 666 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C 666 " --> pdb=" O TRP C 659 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 632 through 636 removed outlier: 7.211A pdb=" N ILE A 640 " --> pdb=" O ALA C 634 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLY C 636 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLU A 642 " --> pdb=" O GLY C 636 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 655 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 654 " --> pdb=" O PHE B 672 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASP B 658 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N TYR B 668 " --> pdb=" O ASP B 658 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 677 " --> pdb=" O ARG C 683 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 632 through 634 removed outlier: 6.242A pdb=" N VAL B 632 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU C 642 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ALA B 634 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TRP C 644 " --> pdb=" O ALA B 634 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 653 " --> pdb=" O GLN C 639 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N PHE C 641 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA A 655 " --> pdb=" O PHE C 641 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER C 643 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG A 657 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE A 672 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 655 " --> pdb=" O TYR A 670 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR A 670 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 657 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 668 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TRP A 659 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN A 666 " --> pdb=" O TRP A 659 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA A 677 " --> pdb=" O ARG B 683 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 698 removed outlier: 3.532A pdb=" N SER A 694 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 716 " --> pdb=" O SER A 698 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 713 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER A 735 " --> pdb=" O ASN A 806 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASN A 806 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR A 737 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 804 " --> pdb=" O THR A 737 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 813 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 764 " --> pdb=" O GLY A 813 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 707 through 708 removed outlier: 7.522A pdb=" N LEU A 744 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A 789 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 268 through 269 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 268 through 269 current: chain 'B' and resid 369 through 377 removed outlier: 7.044A pdb=" N GLU B 394 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS B 372 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 396 " --> pdb=" O LYS B 372 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 415 through 416 current: chain 'B' and resid 543 through 548 removed outlier: 7.221A pdb=" N ILE B 568 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASP B 545 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 282 through 285 removed outlier: 6.924A pdb=" N MET B 354 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 358 " --> pdb=" O LEU B 320 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 353 through 358 current: chain 'B' and resid 381 through 390 removed outlier: 6.331A pdb=" N ILE B 381 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 407 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG B 383 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLN B 409 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL B 385 " --> pdb=" O GLN B 409 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLU B 411 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N GLY B 387 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 428 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLY B 406 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 557 through 559 removed outlier: 3.615A pdb=" N GLU B 609 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 693 through 698 removed outlier: 3.609A pdb=" N SER B 694 " --> pdb=" O ARG B 720 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 696 " --> pdb=" O TRP B 718 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP B 718 " --> pdb=" O GLY B 696 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 816 " --> pdb=" O MET B 725 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER B 735 " --> pdb=" O ASN B 806 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 806 " --> pdb=" O SER B 735 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR B 737 " --> pdb=" O THR B 804 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR B 804 " --> pdb=" O THR B 737 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 707 through 708 removed outlier: 7.606A pdb=" N LEU B 744 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU B 789 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 746 " --> pdb=" O VAL B 787 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 779 " --> pdb=" O ARG B 788 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 268 through 269 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 268 through 269 current: chain 'C' and resid 313 through 320 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 313 through 320 current: chain 'C' and resid 404 through 416 removed outlier: 7.828A pdb=" N VAL C 428 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY C 406 " --> pdb=" O VAL C 428 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 427 through 429 current: chain 'C' and resid 557 through 559 Processing sheet with id=AC1, first strand: chain 'C' and resid 274 through 276 removed outlier: 5.954A pdb=" N ILE C 336 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 376 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS C 402 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 397 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR C 422 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE C 399 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 419 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 467 " --> pdb=" O LYS C 548 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 568 " --> pdb=" O ILE C 543 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP C 545 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 574 " --> pdb=" O THR C 549 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 615 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASN C 570 " --> pdb=" O GLU C 615 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN C 617 " --> pdb=" O ASN C 570 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET C 572 " --> pdb=" O GLN C 617 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 619 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLU C 574 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE C 621 " --> pdb=" O GLU C 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 693 through 698 removed outlier: 3.742A pdb=" N LYS C 713 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 813 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 707 through 708 Processing sheet with id=AC4, first strand: chain 'C' and resid 735 through 738 Processing sheet with id=AC5, first strand: chain 'C' and resid 776 through 780 294 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.64 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: 4254 1.33 - 1.45: 2821 1.45 - 1.57: 8322 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 15482 Sorted by residual: bond pdb=" N VAL C 774 " pdb=" CA VAL C 774 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.36e+00 bond pdb=" C PRO C 446 " pdb=" O PRO C 446 " ideal model delta sigma weight residual 1.240 1.212 0.029 1.12e-02 7.97e+03 6.56e+00 bond pdb=" N GLU A 358 " pdb=" CA GLU A 358 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.54e+00 bond pdb=" N MET A 445 " pdb=" CA MET A 445 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.30e-02 5.92e+03 6.36e+00 bond pdb=" N LEU C 776 " pdb=" CA LEU C 776 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.33e-02 5.65e+03 6.30e+00 ... (remaining 15477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 20379 1.41 - 2.82: 608 2.82 - 4.23: 110 4.23 - 5.64: 11 5.64 - 7.05: 5 Bond angle restraints: 21113 Sorted by residual: angle pdb=" N PRO C 446 " pdb=" CA PRO C 446 " pdb=" C PRO C 446 " ideal model delta sigma weight residual 110.70 116.99 -6.29 1.22e+00 6.72e-01 2.66e+01 angle pdb=" N THR A 449 " pdb=" CA THR A 449 " pdb=" C THR A 449 " ideal model delta sigma weight residual 113.21 107.62 5.59 1.40e+00 5.10e-01 1.60e+01 angle pdb=" N ASP B 478 " pdb=" CA ASP B 478 " pdb=" C ASP B 478 " ideal model delta sigma weight residual 112.54 107.73 4.81 1.22e+00 6.72e-01 1.55e+01 angle pdb=" N TYR A 448 " pdb=" CA TYR A 448 " pdb=" C TYR A 448 " ideal model delta sigma weight residual 112.86 108.74 4.12 1.22e+00 6.72e-01 1.14e+01 angle pdb=" C PRO B 446 " pdb=" N PRO B 447 " pdb=" CA PRO B 447 " ideal model delta sigma weight residual 119.84 115.90 3.94 1.25e+00 6.40e-01 9.93e+00 ... (remaining 21108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8218 17.95 - 35.89: 637 35.89 - 53.84: 102 53.84 - 71.78: 23 71.78 - 89.73: 13 Dihedral angle restraints: 8993 sinusoidal: 3442 harmonic: 5551 Sorted by residual: dihedral pdb=" CA PRO B 446 " pdb=" C PRO B 446 " pdb=" N PRO B 447 " pdb=" CA PRO B 447 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA VAL B 605 " pdb=" C VAL B 605 " pdb=" N TRP B 606 " pdb=" CA TRP B 606 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR B 685 " pdb=" C TYR B 685 " pdb=" N THR B 686 " pdb=" CA THR B 686 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1456 0.036 - 0.072: 577 0.072 - 0.107: 214 0.107 - 0.143: 106 0.143 - 0.179: 2 Chirality restraints: 2355 Sorted by residual: chirality pdb=" CA GLU B 394 " pdb=" N GLU B 394 " pdb=" C GLU B 394 " pdb=" CB GLU B 394 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA MET A 445 " pdb=" N MET A 445 " pdb=" C MET A 445 " pdb=" CB MET A 445 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE A 568 " pdb=" N ILE A 568 " pdb=" C ILE A 568 " pdb=" CB ILE A 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 2352 not shown) Planarity restraints: 2707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 446 " 0.039 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO B 447 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 447 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 447 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 396 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" CG ASP A 396 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP A 396 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 396 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 294 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO C 295 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.026 5.00e-02 4.00e+02 ... (remaining 2704 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1584 2.75 - 3.29: 14317 3.29 - 3.83: 24391 3.83 - 4.36: 29932 4.36 - 4.90: 52413 Nonbonded interactions: 122637 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 396 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 766 " pdb=" NH1 ARG C 790 " model vdw 2.224 3.120 nonbonded pdb=" OG SER B 503 " pdb=" OE1 GLU B 504 " model vdw 2.228 3.040 nonbonded pdb=" OG SER C 331 " pdb=" O ASP C 396 " model vdw 2.245 3.040 nonbonded pdb=" O ALA A 801 " pdb=" OH TYR A 805 " model vdw 2.250 3.040 ... (remaining 122632 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 198 through 820) selection = chain 'B' selection = (chain 'C' and resid 198 through 820) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.010 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.490 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.004 0.037 15482 Z= 0.182 Angle : 0.593 7.046 21113 Z= 0.332 Chirality : 0.048 0.179 2355 Planarity : 0.004 0.058 2707 Dihedral : 13.424 89.731 5517 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.50 % Allowed : 0.31 % Favored : 99.19 % 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: -2.13 (0.18), residues: 1943 helix: -1.19 (0.39), residues: 168 sheet: -1.29 (0.23), residues: 533 loop : -1.53 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 529 TYR 0.019 0.001 TYR A 444 PHE 0.007 0.001 PHE C 253 TRP 0.012 0.001 TRP A 599 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (15482) covalent geometry : angle 0.59261 / 0.33 (21113) hydrogen bonds : bond 0.28105 / 18.97 ( 294) hydrogen bonds : angle 10.43551 / 7.27 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 218 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 543 ILE cc_start: 0.7817 (mp) cc_final: 0.7528 (mt) REVERT: A 551 ILE cc_start: 0.8100 (mm) cc_final: 0.7753 (mm) REVERT: B 564 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7316 (tp40) REVERT: B 807 ASN cc_start: 0.7730 (m-40) cc_final: 0.7439 (p0) REVERT: C 296 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6133 (mm-30) REVERT: C 417 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7440 (mmt90) REVERT: C 806 ASN cc_start: 0.7605 (p0) cc_final: 0.7328 (p0) REVERT: I 147 LYS cc_start: 0.5674 (OUTLIER) cc_final: 0.3938 (mmtm) outliers start: 8 outliers final: 2 residues processed: 223 average time/residue: 0.1171 time to fit residues: 39.3965 Evaluate side-chains 163 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain I residue 147 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN A 539 ASN A 561 ASN A 806 ASN ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113498 restraints weight = 23943.590| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.98 r_work: 0.3331 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15482 Z= 0.214 Angle : 0.640 7.886 21113 Z= 0.344 Chirality : 0.050 0.169 2355 Planarity : 0.005 0.055 2707 Dihedral : 5.680 88.676 2201 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.80 % Allowed : 9.15 % Favored : 89.05 % 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: -2.06 (0.18), residues: 1943 helix: -0.69 (0.37), residues: 191 sheet: -1.24 (0.22), residues: 554 loop : -1.57 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 364 TYR 0.023 0.002 TYR B 798 PHE 0.011 0.001 PHE C 253 TRP 0.013 0.002 TRP B 599 HIS 0.005 0.002 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (15482) covalent geometry : angle 0.63963 / 0.34 (21113) hydrogen bonds : bond 0.05006 / 3.36 ( 294) hydrogen bonds : angle 6.87865 / 4.74 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 543 ILE cc_start: 0.8195 (mp) cc_final: 0.7885 (mt) REVERT: B 395 ASP cc_start: 0.8091 (t0) cc_final: 0.7882 (t0) REVERT: B 573 ILE cc_start: 0.8847 (mp) cc_final: 0.8556 (mt) REVERT: B 712 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 732 GLU cc_start: 0.7596 (pm20) cc_final: 0.7035 (pm20) REVERT: B 807 ASN cc_start: 0.7888 (m-40) cc_final: 0.7596 (p0) REVERT: C 296 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6736 (mm-30) REVERT: C 806 ASN cc_start: 0.7839 (p0) cc_final: 0.7436 (p0) outliers start: 29 outliers final: 26 residues processed: 191 average time/residue: 0.0972 time to fit residues: 28.6675 Evaluate side-chains 182 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [192, 85, 74, 146, 64, 141, 119, 132, 62, 111, 171] chunk 192 optimal weight: 0.0000 chunk 85 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN A 409 GLN A 498 ASN A 542 ASN C 511 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112304 restraints weight = 24291.787| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.99 r_work: 0.3309 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15482 Z= 0.238 Angle : 0.652 7.535 21113 Z= 0.351 Chirality : 0.050 0.173 2355 Planarity : 0.005 0.058 2707 Dihedral : 5.825 88.686 2197 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.61 % Allowed : 12.82 % Favored : 84.57 % 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: -2.14 (0.18), residues: 1943 helix: -0.82 (0.36), residues: 197 sheet: -1.23 (0.22), residues: 556 loop : -1.65 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 364 TYR 0.022 0.002 TYR A 444 PHE 0.014 0.002 PHE C 253 TRP 0.013 0.002 TRP B 599 HIS 0.006 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (15482) covalent geometry : angle 0.65201 / 0.35 (21113) hydrogen bonds : bond 0.04996 / 3.39 ( 294) hydrogen bonds : angle 6.51272 / 4.49 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.581 Fit side-chains REVERT: A 396 ASP cc_start: 0.8367 (t0) cc_final: 0.8090 (t0) REVERT: A 500 ARG cc_start: 0.7186 (mtp180) cc_final: 0.6419 (ptt180) REVERT: A 543 ILE cc_start: 0.8234 (mp) cc_final: 0.7961 (mt) REVERT: B 358 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: B 573 ILE cc_start: 0.8880 (mp) cc_final: 0.8661 (mt) REVERT: B 712 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 732 GLU cc_start: 0.7619 (pm20) cc_final: 0.7003 (pm20) REVERT: B 807 ASN cc_start: 0.7837 (m-40) cc_final: 0.7607 (p0) REVERT: C 212 MET cc_start: 0.7955 (ttt) cc_final: 0.7625 (ttt) REVERT: C 296 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6830 (mm-30) outliers start: 42 outliers final: 37 residues processed: 201 average time/residue: 0.1020 time to fit residues: 32.0145 Evaluate side-chains 187 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [36, 183, 61, 161, 62, 64, 77, 132, 154, 127, 135] chunk 36 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 HIS B 666 GLN C 511 GLN C 692 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112237 restraints weight = 24081.107| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.99 r_work: 0.3311 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15482 Z= 0.228 Angle : 0.637 6.977 21113 Z= 0.342 Chirality : 0.049 0.171 2355 Planarity : 0.005 0.058 2707 Dihedral : 5.773 85.027 2197 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.17 % Allowed : 14.81 % Favored : 82.02 % 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: -2.12 (0.18), residues: 1943 helix: -0.71 (0.37), residues: 197 sheet: -1.20 (0.22), residues: 568 loop : -1.66 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 657 TYR 0.022 0.002 TYR A 444 PHE 0.013 0.002 PHE C 253 TRP 0.013 0.002 TRP B 599 HIS 0.005 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (15482) covalent geometry : angle 0.63661 / 0.34 (21113) hydrogen bonds : bond 0.04628 / 3.14 ( 294) hydrogen bonds : angle 6.30412 / 4.34 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.579 Fit side-chains REVERT: A 396 ASP cc_start: 0.8464 (t0) cc_final: 0.7962 (t0) REVERT: A 543 ILE cc_start: 0.8229 (mp) cc_final: 0.7980 (mt) REVERT: B 573 ILE cc_start: 0.8886 (mp) cc_final: 0.8672 (mt) REVERT: B 712 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 732 GLU cc_start: 0.7665 (pm20) cc_final: 0.7121 (pm20) REVERT: C 212 MET cc_start: 0.7925 (ttt) cc_final: 0.7653 (ttt) REVERT: C 296 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7020 (mm-30) outliers start: 51 outliers final: 41 residues processed: 199 average time/residue: 0.1005 time to fit residues: 31.1265 Evaluate side-chains 193 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [69, 147, 14, 153, 7, 74, 94, 23, 98, 117, 167] chunk 69 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 117 optimal weight: 30.0000 chunk 167 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 807 ASN C 511 GLN C 806 ASN C 807 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112861 restraints weight = 23984.582| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.00 r_work: 0.3322 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15482 Z= 0.183 Angle : 0.590 6.541 21113 Z= 0.317 Chirality : 0.048 0.162 2355 Planarity : 0.005 0.057 2707 Dihedral : 5.150 35.067 2194 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.80 % Allowed : 16.43 % Favored : 79.78 % 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: -1.99 (0.18), residues: 1943 helix: -0.46 (0.38), residues: 197 sheet: -1.16 (0.23), residues: 558 loop : -1.58 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 364 TYR 0.022 0.002 TYR A 444 PHE 0.011 0.001 PHE C 253 TRP 0.012 0.002 TRP B 599 HIS 0.004 0.001 HIS C 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (15482) covalent geometry : angle 0.58966 / 0.32 (21113) hydrogen bonds : bond 0.04166 / 2.81 ( 294) hydrogen bonds : angle 6.10530 / 4.22 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 161 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8431 (t0) cc_final: 0.8107 (t0) REVERT: B 269 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 712 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7469 (tm-30) REVERT: B 732 GLU cc_start: 0.7601 (pm20) cc_final: 0.6883 (pm20) REVERT: C 212 MET cc_start: 0.7855 (ttt) cc_final: 0.7560 (ttt) REVERT: C 269 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7994 (mp) REVERT: C 296 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6912 (mm-30) REVERT: C 332 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: C 449 THR cc_start: 0.6883 (OUTLIER) cc_final: 0.6683 (m) REVERT: C 796 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7398 (pm20) outliers start: 61 outliers final: 48 residues processed: 211 average time/residue: 0.1064 time to fit residues: 34.9298 Evaluate side-chains 204 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 807 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [143, 24, 2, 15, 142, 60, 122, 27, 180, 74, 106] chunk 143 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 15 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 180 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 807 ASN C 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112756 restraints weight = 24117.657| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.95 r_work: 0.3319 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15482 Z= 0.203 Angle : 0.607 6.363 21113 Z= 0.327 Chirality : 0.048 0.165 2355 Planarity : 0.005 0.057 2707 Dihedral : 5.184 35.141 2194 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.98 % Allowed : 17.36 % Favored : 78.66 % 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: -2.00 (0.18), residues: 1943 helix: -0.51 (0.38), residues: 198 sheet: -1.14 (0.22), residues: 571 loop : -1.60 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 364 TYR 0.022 0.002 TYR A 444 PHE 0.012 0.001 PHE C 253 TRP 0.012 0.002 TRP B 599 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (15482) covalent geometry : angle 0.60730 / 0.33 (21113) hydrogen bonds : bond 0.04264 / 2.89 ( 294) hydrogen bonds : angle 6.09318 / 4.21 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8377 (t0) cc_final: 0.8020 (t0) REVERT: B 269 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 358 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: B 435 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7135 (pt0) REVERT: B 712 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7564 (tm-30) REVERT: B 732 GLU cc_start: 0.7608 (pm20) cc_final: 0.6951 (pm20) REVERT: C 212 MET cc_start: 0.7880 (ttt) cc_final: 0.7615 (ttt) REVERT: C 269 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8011 (mp) REVERT: C 296 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 332 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: C 449 THR cc_start: 0.6856 (OUTLIER) cc_final: 0.6624 (m) outliers start: 64 outliers final: 53 residues processed: 208 average time/residue: 0.1009 time to fit residues: 32.9772 Evaluate side-chains 211 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [133, 154, 105, 70, 168, 128, 138, 161, 166, 6, 147] chunk 133 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 166 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 617 GLN C 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114562 restraints weight = 23737.196| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.95 r_work: 0.3346 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15482 Z= 0.136 Angle : 0.548 6.462 21113 Z= 0.294 Chirality : 0.047 0.152 2355 Planarity : 0.004 0.055 2707 Dihedral : 4.791 32.313 2194 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.42 % Allowed : 18.17 % Favored : 78.41 % 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: -1.83 (0.19), residues: 1943 helix: -0.14 (0.39), residues: 197 sheet: -1.12 (0.22), residues: 560 loop : -1.47 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 364 TYR 0.018 0.001 TYR A 444 PHE 0.008 0.001 PHE C 253 TRP 0.012 0.001 TRP B 599 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (15482) covalent geometry : angle 0.54834 / 0.29 (21113) hydrogen bonds : bond 0.03612 / 2.43 ( 294) hydrogen bonds : angle 5.88308 / 4.08 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 241 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7776 (m) REVERT: A 396 ASP cc_start: 0.8327 (t70) cc_final: 0.7938 (t0) REVERT: A 814 ILE cc_start: 0.8835 (pt) cc_final: 0.8513 (tt) REVERT: B 269 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 435 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: B 712 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7521 (tm-30) REVERT: B 732 GLU cc_start: 0.7629 (pm20) cc_final: 0.6978 (pm20) REVERT: C 212 MET cc_start: 0.7858 (ttt) cc_final: 0.7524 (ttt) REVERT: C 269 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8033 (mp) REVERT: C 296 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 332 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: C 449 THR cc_start: 0.6908 (OUTLIER) cc_final: 0.6651 (m) REVERT: C 796 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7471 (pm20) outliers start: 55 outliers final: 41 residues processed: 205 average time/residue: 0.1022 time to fit residues: 32.9608 Evaluate side-chains 201 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 160 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [52, 98, 192, 65, 76, 54, 179, 49, 36, 8, 83] chunk 52 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 511 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113355 restraints weight = 24068.103| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.00 r_work: 0.3326 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15482 Z= 0.174 Angle : 0.580 6.329 21113 Z= 0.311 Chirality : 0.048 0.158 2355 Planarity : 0.005 0.055 2707 Dihedral : 4.896 32.495 2192 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.73 % Allowed : 18.17 % Favored : 78.10 % 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: -1.87 (0.19), residues: 1943 helix: -0.25 (0.39), residues: 198 sheet: -1.11 (0.23), residues: 553 loop : -1.50 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 364 TYR 0.020 0.001 TYR A 444 PHE 0.011 0.001 PHE C 253 TRP 0.012 0.001 TRP B 599 HIS 0.004 0.001 HIS C 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (15482) covalent geometry : angle 0.57969 / 0.31 (21113) hydrogen bonds : bond 0.03944 / 2.68 ( 294) hydrogen bonds : angle 5.90514 / 4.08 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 241 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7801 (m) REVERT: A 396 ASP cc_start: 0.8397 (t70) cc_final: 0.7967 (t0) REVERT: A 814 ILE cc_start: 0.8875 (pt) cc_final: 0.8556 (tt) REVERT: B 269 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.7989 (mp) REVERT: B 358 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: B 435 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7135 (pt0) REVERT: B 712 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 732 GLU cc_start: 0.7633 (pm20) cc_final: 0.6962 (pm20) REVERT: C 212 MET cc_start: 0.7775 (ttt) cc_final: 0.7419 (ttt) REVERT: C 269 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8032 (mp) REVERT: C 296 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7057 (mm-30) REVERT: C 332 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8312 (mp10) REVERT: C 449 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6645 (m) REVERT: C 796 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7458 (pm20) outliers start: 60 outliers final: 49 residues processed: 205 average time/residue: 0.0996 time to fit residues: 32.1004 Evaluate side-chains 212 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [57, 104, 36, 160, 119, 164, 120, 63, 71, 147, 126] chunk 57 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 332 GLN C 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113007 restraints weight = 23843.966| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.98 r_work: 0.3321 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15482 Z= 0.191 Angle : 0.597 6.762 21113 Z= 0.321 Chirality : 0.048 0.161 2355 Planarity : 0.005 0.057 2707 Dihedral : 4.993 33.390 2192 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.92 % Allowed : 18.48 % Favored : 77.60 % 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: -1.89 (0.19), residues: 1943 helix: -0.24 (0.39), residues: 191 sheet: -1.12 (0.22), residues: 565 loop : -1.52 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 364 TYR 0.021 0.002 TYR A 444 PHE 0.011 0.001 PHE C 253 TRP 0.012 0.002 TRP B 599 HIS 0.004 0.001 HIS C 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (15482) covalent geometry : angle 0.59704 / 0.32 (21113) hydrogen bonds : bond 0.04087 / 2.78 ( 294) hydrogen bonds : angle 5.94561 / 4.11 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 241 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7804 (m) REVERT: A 396 ASP cc_start: 0.8387 (t70) cc_final: 0.7954 (t0) REVERT: A 814 ILE cc_start: 0.8882 (pt) cc_final: 0.8605 (tt) REVERT: B 269 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 358 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: B 435 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: B 712 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7584 (tm-30) REVERT: B 732 GLU cc_start: 0.7671 (pm20) cc_final: 0.7006 (pm20) REVERT: C 212 MET cc_start: 0.7763 (ttt) cc_final: 0.7404 (ttt) REVERT: C 269 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8028 (mp) REVERT: C 296 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7064 (mm-30) REVERT: C 332 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8305 (mp10) REVERT: C 449 THR cc_start: 0.6872 (OUTLIER) cc_final: 0.6602 (m) REVERT: C 790 ARG cc_start: 0.7808 (mmt90) cc_final: 0.7532 (mmt90) REVERT: C 796 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7516 (pm20) outliers start: 63 outliers final: 53 residues processed: 203 average time/residue: 0.0974 time to fit residues: 31.2565 Evaluate side-chains 211 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [17, 46, 59, 185, 31, 30, 71, 184, 110, 63, 146] chunk 17 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 511 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112862 restraints weight = 24083.846| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.99 r_work: 0.3321 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15482 Z= 0.194 Angle : 0.602 7.073 21113 Z= 0.323 Chirality : 0.048 0.161 2355 Planarity : 0.005 0.057 2707 Dihedral : 5.027 34.125 2192 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.04 % Allowed : 18.54 % Favored : 77.41 % 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: -1.97 (0.18), residues: 1943 helix: -0.35 (0.38), residues: 198 sheet: -1.19 (0.22), residues: 557 loop : -1.55 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 364 TYR 0.021 0.002 TYR A 444 PHE 0.011 0.001 PHE C 253 TRP 0.012 0.002 TRP B 599 HIS 0.004 0.001 HIS C 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (15482) covalent geometry : angle 0.60205 / 0.32 (21113) hydrogen bonds : bond 0.04103 / 2.79 ( 294) hydrogen bonds : angle 5.95926 / 4.12 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 241 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7786 (m) REVERT: A 396 ASP cc_start: 0.8400 (t70) cc_final: 0.7967 (t0) REVERT: A 814 ILE cc_start: 0.8874 (pt) cc_final: 0.8602 (tt) REVERT: B 269 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7983 (mp) REVERT: B 358 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: B 435 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7173 (pt0) REVERT: B 712 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 732 GLU cc_start: 0.7693 (pm20) cc_final: 0.7030 (pm20) REVERT: C 212 MET cc_start: 0.7761 (ttt) cc_final: 0.7393 (ttt) REVERT: C 269 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8029 (mp) REVERT: C 296 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7042 (mm-30) REVERT: C 332 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8304 (mp10) REVERT: C 790 ARG cc_start: 0.7768 (mmt90) cc_final: 0.7564 (mmt90) REVERT: C 796 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7485 (pm20) outliers start: 65 outliers final: 55 residues processed: 201 average time/residue: 0.0981 time to fit residues: 31.3549 Evaluate side-chains 212 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [178, 31, 169, 90, 29, 13, 70, 65, 69, 48, 77] chunk 178 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 169 optimal weight: 0.0000 chunk 90 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN C 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117082 restraints weight = 23502.907| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.96 r_work: 0.3382 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15482 Z= 0.095 Angle : 0.510 7.397 21113 Z= 0.272 Chirality : 0.046 0.149 2355 Planarity : 0.004 0.053 2707 Dihedral : 4.356 27.996 2192 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.36 % Allowed : 20.04 % Favored : 77.60 % 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: -1.64 (0.19), residues: 1943 helix: 0.11 (0.40), residues: 205 sheet: -1.00 (0.23), residues: 563 loop : -1.36 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 364 TYR 0.012 0.001 TYR B 356 PHE 0.005 0.001 PHE B 672 TRP 0.012 0.001 TRP B 599 HIS 0.004 0.001 HIS C 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (15482) covalent geometry : angle 0.51021 / 0.27 (21113) hydrogen bonds : bond 0.02980 / 1.97 ( 294) hydrogen bonds : angle 5.61505 / 3.91 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.39 seconds wall clock time: 68 minutes 9.83 seconds (4089.83 seconds total)