Starting phenix.real_space_refine on Thu Feb 5 17:52:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfe_49364/02_2026/9nfe_49364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfe_49364/02_2026/9nfe_49364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nfe_49364/02_2026/9nfe_49364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfe_49364/02_2026/9nfe_49364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nfe_49364/02_2026/9nfe_49364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfe_49364/02_2026/9nfe_49364.map" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 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 90 5.16 5 C 11874 2.51 5 N 3177 2.21 5 O 3447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18588 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6196 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 38, 'TRANS': 729} Chain: "B" Number of atoms: 6196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6196 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 38, 'TRANS': 729} Chain: "C" Number of atoms: 6196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6196 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 38, 'TRANS': 729} Time building chain proxies: 4.29, per 1000 atoms: 0.23 Number of scatterers: 18588 At special positions: 0 Unit cell: (129.31, 133.33, 95.81, 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 90 16.00 O 3447 8.00 N 3177 7.00 C 11874 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: 1.47 Conformation dependent library (CDL) restraints added in 817.6 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4278 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 30 sheets defined 31.5% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.511A pdb=" N ARG A 89 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.777A pdb=" N ALA A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.638A pdb=" N ILE A 179 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 375 through 391 removed outlier: 3.715A pdb=" N HIS A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.820A pdb=" N PHE A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 Processing helix chain 'A' and resid 465 through 472 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 481 through 484 Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.617A pdb=" N ARG A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.615A pdb=" N VAL A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.663A pdb=" N LEU A 526 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.712A pdb=" N VAL A 574 " --> pdb=" O PRO A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.745A pdb=" N ASN A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 618 removed outlier: 3.888A pdb=" N THR A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 613 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 616 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.965A pdb=" N TYR A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 688 " --> pdb=" O TYR A 684 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 689 " --> pdb=" O TYR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 65 through 73 Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.536A pdb=" N ARG B 89 " --> pdb=" O TYR B 86 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.753A pdb=" N ALA B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 375 through 391 removed outlier: 3.781A pdb=" N HIS B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLU B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 removed outlier: 3.844A pdb=" N PHE B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 452 removed outlier: 3.532A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 481 through 484 Processing helix chain 'B' and resid 485 through 491 removed outlier: 3.662A pdb=" N ARG B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 491 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 Processing helix chain 'B' and resid 513 through 520 removed outlier: 3.511A pdb=" N GLU B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.680A pdb=" N LEU B 526 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.740A pdb=" N VAL B 574 " --> pdb=" O PRO B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.742A pdb=" N ASN B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 618 removed outlier: 4.112A pdb=" N THR B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 Processing helix chain 'B' and resid 680 through 688 removed outlier: 3.960A pdb=" N TYR B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 688 " --> pdb=" O TYR B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 793 Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 83 through 92 Proline residue: C 90 - end of helix Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.782A pdb=" N ALA C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 372 through 378 removed outlier: 4.469A pdb=" N ALA C 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 391 Processing helix chain 'C' and resid 405 through 416 removed outlier: 3.865A pdb=" N PHE C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 452 Processing helix chain 'C' and resid 465 through 472 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 481 through 484 Processing helix chain 'C' and resid 485 through 490 removed outlier: 3.667A pdb=" N ARG C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 500 Processing helix chain 'C' and resid 513 through 520 removed outlier: 3.525A pdb=" N GLU C 518 " --> pdb=" O PRO C 514 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 526 removed outlier: 3.680A pdb=" N LEU C 526 " --> pdb=" O ASP C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 545 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 586 through 595 removed outlier: 3.745A pdb=" N ASN C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 618 removed outlier: 4.054A pdb=" N THR C 610 " --> pdb=" O ASN C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 649 Processing helix chain 'C' and resid 680 through 688 removed outlier: 3.986A pdb=" N TYR C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN C 688 " --> pdb=" O TYR C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 793 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 62 removed outlier: 8.949A pdb=" N ARG A 31 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 101 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 124 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER A 135 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 126 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 235 removed outlier: 5.865A pdb=" N ILE A 224 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 250 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 242 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 234 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU A 240 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 278 removed outlier: 5.082A pdb=" N GLN A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG A 267 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A 323 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP A 315 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 321 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 339 removed outlier: 3.759A pdb=" N GLN A 349 " --> pdb=" O ASP A 339 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A 352 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 505 through 506 removed outlier: 8.299A pdb=" N LEU A 506 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP A 460 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 419 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP A 460 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN A 421 " --> pdb=" O TRP A 460 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 394 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA A 361 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TRP A 658 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 363 " --> pdb=" O TRP A 658 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 551 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 577 through 578 removed outlier: 4.146A pdb=" N GLN A 578 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 693 through 699 removed outlier: 6.535A pdb=" N VAL A 708 " --> pdb=" O GLU A 745 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU A 745 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN A 710 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N MET A 743 " --> pdb=" O ASN A 710 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 730 through 738 removed outlier: 6.185A pdb=" N GLN A 730 " --> pdb=" O ASP A 724 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP A 724 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AB3, first strand: chain 'B' and resid 56 through 62 removed outlier: 8.931A pdb=" N ARG B 31 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR B 101 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 124 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER B 135 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 126 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AB5, first strand: chain 'B' and resid 223 through 235 removed outlier: 5.821A pdb=" N ILE B 224 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG B 250 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER B 242 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL B 234 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLU B 240 " --> pdb=" O VAL B 234 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 270 through 278 removed outlier: 5.174A pdb=" N GLN B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 267 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 323 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP B 315 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 321 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 334 through 339 removed outlier: 4.654A pdb=" N PHE B 352 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 505 through 506 removed outlier: 8.255A pdb=" N LEU B 506 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP B 460 " --> pdb=" O LEU B 506 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 419 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP B 460 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN B 421 " --> pdb=" O TRP B 460 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 394 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA B 361 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TRP B 658 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY B 363 " --> pdb=" O TRP B 658 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 551 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 577 through 578 removed outlier: 5.914A pdb=" N MET B 584 " --> pdb=" O GLN B 578 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 693 through 699 removed outlier: 6.366A pdb=" N VAL B 708 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLU B 745 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASN B 710 " --> pdb=" O MET B 743 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N MET B 743 " --> pdb=" O ASN B 710 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 730 through 738 removed outlier: 6.243A pdb=" N GLN B 730 " --> pdb=" O ASP B 724 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 724 " --> pdb=" O GLN B 730 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'C' and resid 56 through 62 removed outlier: 8.969A pdb=" N ARG C 31 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR C 101 " --> pdb=" O ARG C 31 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA C 124 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER C 135 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C 126 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC6, first strand: chain 'C' and resid 223 through 235 removed outlier: 5.838A pdb=" N ILE C 224 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG C 250 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER C 242 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL C 234 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU C 240 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 270 through 278 removed outlier: 5.047A pdb=" N GLN C 271 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG C 267 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP C 323 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP C 315 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 321 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 334 through 339 removed outlier: 4.576A pdb=" N PHE C 352 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 505 through 506 removed outlier: 8.286A pdb=" N LEU C 506 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP C 460 " --> pdb=" O LEU C 506 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 419 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP C 460 " --> pdb=" O VAL C 419 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN C 421 " --> pdb=" O TRP C 460 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 394 " --> pdb=" O LYS C 362 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA C 361 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TRP C 658 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY C 363 " --> pdb=" O TRP C 658 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 551 " --> pdb=" O ILE C 657 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 577 through 578 removed outlier: 4.098A pdb=" N GLN C 578 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 693 through 699 removed outlier: 6.478A pdb=" N VAL C 708 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU C 745 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASN C 710 " --> pdb=" O MET C 743 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N MET C 743 " --> pdb=" O ASN C 710 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 730 through 738 removed outlier: 6.138A pdb=" N GLN C 730 " --> pdb=" O ASP C 724 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP C 724 " --> pdb=" O GLN C 730 " (cutoff:3.500A) 771 hydrogen bonds defined for protein. 2046 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: 3.93 Time building geometry restraints manager: 1.98 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: 4330 1.33 - 1.45: 4257 1.45 - 1.57: 10346 1.57 - 1.69: 0 1.69 - 1.82: 153 Bond restraints: 19086 Sorted by residual: bond pdb=" CA SER C 669 " pdb=" CB SER C 669 " ideal model delta sigma weight residual 1.538 1.480 0.058 1.22e-02 6.72e+03 2.28e+01 bond pdb=" CA SER B 669 " pdb=" CB SER B 669 " ideal model delta sigma weight residual 1.539 1.479 0.060 1.36e-02 5.41e+03 1.96e+01 bond pdb=" CA SER B 631 " pdb=" CB SER B 631 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.55e-02 4.16e+03 1.63e+01 bond pdb=" CA SER B 509 " pdb=" CB SER B 509 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.33e-02 5.65e+03 1.62e+01 bond pdb=" CA SER C 27 " pdb=" CB SER C 27 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.43e-02 4.89e+03 1.60e+01 ... (remaining 19081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 24546 2.30 - 4.60: 1217 4.60 - 6.91: 145 6.91 - 9.21: 27 9.21 - 11.51: 3 Bond angle restraints: 25938 Sorted by residual: angle pdb=" N ALA C 593 " pdb=" CA ALA C 593 " pdb=" C ALA C 593 " ideal model delta sigma weight residual 111.28 103.62 7.66 1.09e+00 8.42e-01 4.94e+01 angle pdb=" N ALA B 593 " pdb=" CA ALA B 593 " pdb=" C ALA B 593 " ideal model delta sigma weight residual 111.28 103.62 7.66 1.09e+00 8.42e-01 4.94e+01 angle pdb=" N ALA A 593 " pdb=" CA ALA A 593 " pdb=" C ALA A 593 " ideal model delta sigma weight residual 111.28 103.81 7.47 1.09e+00 8.42e-01 4.70e+01 angle pdb=" C PRO B 510 " pdb=" CA PRO B 510 " pdb=" CB PRO B 510 " ideal model delta sigma weight residual 111.56 122.18 -10.62 1.65e+00 3.67e-01 4.14e+01 angle pdb=" CA PHE B 102 " pdb=" CB PHE B 102 " pdb=" CG PHE B 102 " ideal model delta sigma weight residual 113.80 120.23 -6.43 1.00e+00 1.00e+00 4.13e+01 ... (remaining 25933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.82: 10745 26.82 - 53.64: 407 53.64 - 80.46: 101 80.46 - 107.28: 3 107.28 - 134.10: 3 Dihedral angle restraints: 11259 sinusoidal: 4560 harmonic: 6699 Sorted by residual: dihedral pdb=" CA TRP A 659 " pdb=" C TRP A 659 " pdb=" N ASN A 660 " pdb=" CA ASN A 660 " ideal model delta harmonic sigma weight residual -180.00 -45.90 -134.10 0 5.00e+00 4.00e-02 7.19e+02 dihedral pdb=" CA TRP C 659 " pdb=" C TRP C 659 " pdb=" N ASN C 660 " pdb=" CA ASN C 660 " ideal model delta harmonic sigma weight residual -180.00 -48.05 -131.95 0 5.00e+00 4.00e-02 6.96e+02 dihedral pdb=" CA TRP B 659 " pdb=" C TRP B 659 " pdb=" N ASN B 660 " pdb=" CA ASN B 660 " ideal model delta harmonic sigma weight residual -180.00 -51.57 -128.43 0 5.00e+00 4.00e-02 6.60e+02 ... (remaining 11256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1943 0.059 - 0.118: 514 0.118 - 0.176: 174 0.176 - 0.235: 65 0.235 - 0.294: 28 Chirality restraints: 2724 Sorted by residual: chirality pdb=" CA TYR B 98 " pdb=" N TYR B 98 " pdb=" C TYR B 98 " pdb=" CB TYR B 98 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ILE B 760 " pdb=" N ILE B 760 " pdb=" C ILE B 760 " pdb=" CB ILE B 760 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA VAL B 367 " pdb=" N VAL B 367 " pdb=" C VAL B 367 " pdb=" CB VAL B 367 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2721 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 100 " 0.577 9.50e-02 1.11e+02 2.59e-01 4.10e+01 pdb=" NE ARG A 100 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 100 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 100 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 100 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 100 " 0.550 9.50e-02 1.11e+02 2.46e-01 3.72e+01 pdb=" NE ARG B 100 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 100 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 100 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 100 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 100 " 0.532 9.50e-02 1.11e+02 2.38e-01 3.48e+01 pdb=" NE ARG C 100 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C 100 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 100 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 100 " 0.017 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2579 2.75 - 3.29: 16306 3.29 - 3.83: 29875 3.83 - 4.36: 38790 4.36 - 4.90: 67290 Nonbonded interactions: 154840 Sorted by model distance: nonbonded pdb=" OD1 ASP C 121 " pdb=" OG1 THR C 122 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP B 121 " pdb=" OG1 THR B 122 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 121 " pdb=" OG1 THR A 122 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR A 564 " pdb=" OD2 ASP A 674 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP A 370 " pdb=" OH TYR A 675 " model vdw 2.273 3.040 ... (remaining 154835 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.530 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 19086 Z= 0.463 Angle : 1.025 11.508 25938 Z= 0.706 Chirality : 0.071 0.294 2724 Planarity : 0.014 0.259 3396 Dihedral : 14.737 134.103 6981 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.38 % Favored : 97.49 % Rotamer: Outliers : 1.15 % Allowed : 8.71 % Favored : 90.14 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.14 % Twisted Proline : 2.44 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2310 helix: 0.97 (0.23), residues: 519 sheet: 1.54 (0.20), residues: 699 loop : -0.61 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 31 TYR 0.033 0.002 TYR B 762 PHE 0.024 0.001 PHE B 102 TRP 0.024 0.002 TRP A 659 HIS 0.008 0.001 HIS C 557 Details of bonding type rmsd covalent geometry : bond 0.00671 (19086) covalent geometry : angle 1.02474 (25938) hydrogen bonds : bond 0.21788 ( 771) hydrogen bonds : angle 7.74730 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.728 Fit side-chains REVERT: A 226 ASP cc_start: 0.8515 (t70) cc_final: 0.8252 (t70) REVERT: B 153 GLU cc_start: 0.8652 (tp30) cc_final: 0.8428 (pm20) outliers start: 23 outliers final: 12 residues processed: 139 average time/residue: 0.7248 time to fit residues: 112.0156 Evaluate side-chains 130 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 708 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 172 HIS A 579 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 172 HIS ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.067457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.052122 restraints weight = 36987.456| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 2.79 r_work: 0.2418 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19086 Z= 0.146 Angle : 0.540 9.929 25938 Z= 0.288 Chirality : 0.045 0.145 2724 Planarity : 0.004 0.041 3396 Dihedral : 5.152 55.523 2563 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.69 % Favored : 98.18 % Rotamer: Outliers : 1.05 % Allowed : 9.11 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2310 helix: 1.27 (0.23), residues: 537 sheet: 1.50 (0.20), residues: 696 loop : -0.59 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 31 TYR 0.009 0.001 TYR A 98 PHE 0.015 0.001 PHE C 253 TRP 0.030 0.001 TRP A 659 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00335 (19086) covalent geometry : angle 0.53960 (25938) hydrogen bonds : bond 0.04331 ( 771) hydrogen bonds : angle 5.57966 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.758 Fit side-chains REVERT: A 705 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7723 (tpt) REVERT: B 557 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.8260 (t-90) REVERT: C 557 HIS cc_start: 0.9041 (OUTLIER) cc_final: 0.8274 (t-90) outliers start: 21 outliers final: 4 residues processed: 144 average time/residue: 0.6562 time to fit residues: 105.6054 Evaluate side-chains 121 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 557 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 34 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 179 optimal weight: 0.3980 chunk 229 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN C 156 ASN C 579 ASN ** C 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.065914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.050560 restraints weight = 37497.498| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 2.79 r_work: 0.2386 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2260 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19086 Z= 0.202 Angle : 0.546 9.796 25938 Z= 0.291 Chirality : 0.046 0.149 2724 Planarity : 0.004 0.037 3396 Dihedral : 5.053 55.835 2555 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 1.10 % Allowed : 9.76 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2310 helix: 1.36 (0.23), residues: 537 sheet: 1.35 (0.20), residues: 705 loop : -0.59 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 31 TYR 0.012 0.001 TYR B 98 PHE 0.019 0.001 PHE A 253 TRP 0.014 0.001 TRP A 659 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00475 (19086) covalent geometry : angle 0.54562 (25938) hydrogen bonds : bond 0.04383 ( 771) hydrogen bonds : angle 5.25907 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.784 Fit side-chains REVERT: A 340 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 594 ASN cc_start: 0.6475 (t0) cc_final: 0.6086 (t0) REVERT: A 705 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7909 (tpt) REVERT: B 346 GLN cc_start: 0.8655 (mt0) cc_final: 0.8330 (tm-30) REVERT: B 557 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8147 (t-90) REVERT: C 557 HIS cc_start: 0.9116 (OUTLIER) cc_final: 0.8270 (t-90) outliers start: 22 outliers final: 9 residues processed: 142 average time/residue: 0.7494 time to fit residues: 118.4624 Evaluate side-chains 130 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 670 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 122 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 346 GLN C 579 ASN ** C 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.066506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.051176 restraints weight = 37487.963| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 2.80 r_work: 0.2400 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19086 Z= 0.161 Angle : 0.516 9.246 25938 Z= 0.275 Chirality : 0.045 0.144 2724 Planarity : 0.004 0.038 3396 Dihedral : 4.943 56.459 2555 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.77 % Favored : 98.10 % Rotamer: Outliers : 1.70 % Allowed : 9.96 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2310 helix: 1.43 (0.23), residues: 537 sheet: 1.29 (0.20), residues: 714 loop : -0.65 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 31 TYR 0.010 0.001 TYR B 762 PHE 0.014 0.001 PHE A 253 TRP 0.011 0.001 TRP C 659 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00377 (19086) covalent geometry : angle 0.51557 (25938) hydrogen bonds : bond 0.03821 ( 771) hydrogen bonds : angle 5.11051 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.835 Fit side-chains REVERT: A 340 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7615 (mt-10) REVERT: B 346 GLN cc_start: 0.8703 (mt0) cc_final: 0.8379 (tm-30) REVERT: B 557 HIS cc_start: 0.9037 (OUTLIER) cc_final: 0.8108 (t-90) REVERT: C 346 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: C 557 HIS cc_start: 0.9071 (OUTLIER) cc_final: 0.8190 (t-90) outliers start: 34 outliers final: 11 residues processed: 146 average time/residue: 0.7002 time to fit residues: 114.5222 Evaluate side-chains 132 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 670 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 217 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 579 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 346 GLN C 579 ASN C 594 ASN C 660 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.067727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.052494 restraints weight = 37070.376| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 2.79 r_work: 0.2441 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19086 Z= 0.113 Angle : 0.487 9.140 25938 Z= 0.259 Chirality : 0.044 0.141 2724 Planarity : 0.003 0.039 3396 Dihedral : 4.773 56.730 2555 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.56 % Favored : 98.31 % Rotamer: Outliers : 1.80 % Allowed : 10.21 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2310 helix: 1.57 (0.23), residues: 534 sheet: 1.24 (0.20), residues: 714 loop : -0.62 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 31 TYR 0.010 0.001 TYR A 762 PHE 0.012 0.001 PHE B 36 TRP 0.010 0.001 TRP C 659 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00260 (19086) covalent geometry : angle 0.48661 (25938) hydrogen bonds : bond 0.03318 ( 771) hydrogen bonds : angle 4.98639 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.687 Fit side-chains REVERT: A 340 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7556 (mt-10) REVERT: B 346 GLN cc_start: 0.8730 (mt0) cc_final: 0.8401 (tm-30) REVERT: B 557 HIS cc_start: 0.9046 (OUTLIER) cc_final: 0.8150 (t-90) REVERT: B 594 ASN cc_start: 0.6250 (t0) cc_final: 0.5965 (t0) REVERT: C 346 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: C 557 HIS cc_start: 0.9063 (OUTLIER) cc_final: 0.8249 (t-90) outliers start: 36 outliers final: 15 residues processed: 151 average time/residue: 0.7221 time to fit residues: 121.7337 Evaluate side-chains 134 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 696 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 166 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 579 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 346 GLN C 579 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.065095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.049800 restraints weight = 37535.953| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 2.78 r_work: 0.2372 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2248 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19086 Z= 0.253 Angle : 0.556 9.410 25938 Z= 0.297 Chirality : 0.046 0.149 2724 Planarity : 0.004 0.038 3396 Dihedral : 5.013 56.279 2555 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.56 % Favored : 98.31 % Rotamer: Outliers : 1.50 % Allowed : 10.66 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2310 helix: 1.40 (0.23), residues: 537 sheet: 1.20 (0.20), residues: 702 loop : -0.67 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 31 TYR 0.011 0.001 TYR B 98 PHE 0.021 0.001 PHE A 253 TRP 0.008 0.001 TRP B 297 HIS 0.004 0.001 HIS C 772 Details of bonding type rmsd covalent geometry : bond 0.00605 (19086) covalent geometry : angle 0.55624 (25938) hydrogen bonds : bond 0.04294 ( 771) hydrogen bonds : angle 5.09230 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.894 Fit side-chains REVERT: A 340 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 346 GLN cc_start: 0.8715 (mt0) cc_final: 0.8399 (tm-30) REVERT: B 557 HIS cc_start: 0.9112 (OUTLIER) cc_final: 0.8178 (t-90) REVERT: C 346 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: C 557 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8288 (t-90) outliers start: 30 outliers final: 11 residues processed: 140 average time/residue: 0.7417 time to fit residues: 115.4284 Evaluate side-chains 130 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 670 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 33 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 346 GLN C 579 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.066841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.051540 restraints weight = 37551.216| |-----------------------------------------------------------------------------| r_work (start): 0.2548 rms_B_bonded: 2.81 r_work: 0.2414 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19086 Z= 0.131 Angle : 0.496 7.189 25938 Z= 0.264 Chirality : 0.044 0.144 2724 Planarity : 0.003 0.046 3396 Dihedral : 4.861 57.368 2555 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.55 % Allowed : 11.06 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2310 helix: 1.47 (0.23), residues: 537 sheet: 1.20 (0.20), residues: 696 loop : -0.64 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.009 0.001 TYR A 762 PHE 0.012 0.001 PHE C 253 TRP 0.009 0.001 TRP C 460 HIS 0.002 0.001 HIS B 772 Details of bonding type rmsd covalent geometry : bond 0.00307 (19086) covalent geometry : angle 0.49606 (25938) hydrogen bonds : bond 0.03498 ( 771) hydrogen bonds : angle 4.97133 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.793 Fit side-chains REVERT: A 340 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 469 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 594 ASN cc_start: 0.6131 (t0) cc_final: 0.5910 (t0) REVERT: B 346 GLN cc_start: 0.8751 (mt0) cc_final: 0.8438 (tm-30) REVERT: B 557 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.8120 (t-90) REVERT: C 346 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: C 557 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8204 (t-90) outliers start: 31 outliers final: 14 residues processed: 143 average time/residue: 0.7269 time to fit residues: 115.8626 Evaluate side-chains 134 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 55 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 222 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.067391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.052136 restraints weight = 37274.204| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 2.82 r_work: 0.2432 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19086 Z= 0.104 Angle : 0.473 6.242 25938 Z= 0.251 Chirality : 0.043 0.140 2724 Planarity : 0.003 0.051 3396 Dihedral : 4.727 58.168 2555 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.25 % Allowed : 11.36 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2310 helix: 1.59 (0.23), residues: 534 sheet: 1.17 (0.20), residues: 696 loop : -0.61 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.010 0.001 TYR A 762 PHE 0.011 0.001 PHE B 36 TRP 0.009 0.001 TRP C 460 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00241 (19086) covalent geometry : angle 0.47303 (25938) hydrogen bonds : bond 0.03153 ( 771) hydrogen bonds : angle 4.88368 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.802 Fit side-chains REVERT: A 340 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 469 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 594 ASN cc_start: 0.6125 (t0) cc_final: 0.5911 (t0) REVERT: B 152 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8154 (pttp) REVERT: B 346 GLN cc_start: 0.8755 (mt0) cc_final: 0.8433 (tm-30) REVERT: B 557 HIS cc_start: 0.9046 (OUTLIER) cc_final: 0.8179 (t-90) REVERT: B 584 MET cc_start: 0.8626 (mmt) cc_final: 0.8310 (mmt) REVERT: C 152 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8076 (pttp) REVERT: C 524 GLU cc_start: 0.8499 (mp0) cc_final: 0.8199 (mp0) REVERT: C 557 HIS cc_start: 0.9074 (OUTLIER) cc_final: 0.8176 (t-90) outliers start: 25 outliers final: 11 residues processed: 142 average time/residue: 0.7469 time to fit residues: 117.9125 Evaluate side-chains 134 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 130 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.066212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.050963 restraints weight = 37478.103| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 2.82 r_work: 0.2406 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19086 Z= 0.155 Angle : 0.502 7.246 25938 Z= 0.266 Chirality : 0.044 0.143 2724 Planarity : 0.004 0.056 3396 Dihedral : 4.806 57.842 2555 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.00 % Allowed : 11.81 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2310 helix: 1.52 (0.23), residues: 537 sheet: 1.13 (0.20), residues: 696 loop : -0.61 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.010 0.001 TYR A 762 PHE 0.015 0.001 PHE A 253 TRP 0.008 0.001 TRP A 460 HIS 0.004 0.001 HIS C 772 Details of bonding type rmsd covalent geometry : bond 0.00369 (19086) covalent geometry : angle 0.50234 (25938) hydrogen bonds : bond 0.03567 ( 771) hydrogen bonds : angle 4.92284 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.783 Fit side-chains REVERT: A 340 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 469 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8100 (p) REVERT: B 152 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8161 (pttp) REVERT: B 346 GLN cc_start: 0.8758 (mt0) cc_final: 0.8446 (tm-30) REVERT: B 557 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8117 (t-90) REVERT: C 152 LYS cc_start: 0.8479 (ptpt) cc_final: 0.8091 (pttp) REVERT: C 524 GLU cc_start: 0.8496 (mp0) cc_final: 0.8200 (mp0) REVERT: C 557 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8186 (t-90) outliers start: 20 outliers final: 11 residues processed: 137 average time/residue: 0.7650 time to fit residues: 116.2900 Evaluate side-chains 133 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 196 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN B 54 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.068024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.052811 restraints weight = 37294.721| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 2.81 r_work: 0.2441 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19086 Z= 0.107 Angle : 0.475 7.587 25938 Z= 0.251 Chirality : 0.043 0.139 2724 Planarity : 0.003 0.059 3396 Dihedral : 4.682 58.934 2555 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.00 % Allowed : 11.86 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2310 helix: 1.64 (0.23), residues: 534 sheet: 1.13 (0.20), residues: 696 loop : -0.58 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.010 0.001 TYR A 762 PHE 0.011 0.001 PHE B 36 TRP 0.010 0.001 TRP C 460 HIS 0.002 0.001 HIS C 772 Details of bonding type rmsd covalent geometry : bond 0.00250 (19086) covalent geometry : angle 0.47499 (25938) hydrogen bonds : bond 0.03114 ( 771) hydrogen bonds : angle 4.84241 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.778 Fit side-chains REVERT: A 340 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 469 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.8106 (p) REVERT: A 594 ASN cc_start: 0.5750 (t0) cc_final: 0.5543 (t0) REVERT: B 152 LYS cc_start: 0.8522 (ptpt) cc_final: 0.8145 (pttp) REVERT: B 346 GLN cc_start: 0.8789 (mt0) cc_final: 0.8462 (tm-30) REVERT: B 469 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8157 (p) REVERT: B 557 HIS cc_start: 0.9036 (OUTLIER) cc_final: 0.8125 (t-90) REVERT: C 109 GLU cc_start: 0.8759 (mp0) cc_final: 0.8534 (mp0) REVERT: C 152 LYS cc_start: 0.8475 (ptpt) cc_final: 0.8138 (pttp) REVERT: C 524 GLU cc_start: 0.8489 (mp0) cc_final: 0.8206 (mp0) REVERT: C 557 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.8176 (t-90) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 0.7663 time to fit residues: 122.3418 Evaluate side-chains 135 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 708 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 53 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 221 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN B 54 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.064597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.049413 restraints weight = 37845.368| |-----------------------------------------------------------------------------| r_work (start): 0.2497 rms_B_bonded: 2.78 r_work: 0.2360 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2236 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19086 Z= 0.301 Angle : 0.581 8.209 25938 Z= 0.309 Chirality : 0.048 0.149 2724 Planarity : 0.004 0.061 3396 Dihedral : 5.095 58.279 2555 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.10 % Allowed : 11.86 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2310 helix: 1.35 (0.23), residues: 537 sheet: 1.14 (0.20), residues: 699 loop : -0.69 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 31 TYR 0.011 0.001 TYR B 762 PHE 0.023 0.001 PHE A 253 TRP 0.007 0.001 TRP A 32 HIS 0.006 0.001 HIS C 772 Details of bonding type rmsd covalent geometry : bond 0.00722 (19086) covalent geometry : angle 0.58098 (25938) hydrogen bonds : bond 0.04511 ( 771) hydrogen bonds : angle 5.08879 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5514.61 seconds wall clock time: 95 minutes 12.25 seconds (5712.25 seconds total)