Starting phenix.real_space_refine on Thu Mar 5 15:48:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e89_31012/03_2026/7e89_31012.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e89_31012/03_2026/7e89_31012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e89_31012/03_2026/7e89_31012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e89_31012/03_2026/7e89_31012.map" model { file = "/net/cci-nas-00/data/ceres_data/7e89_31012/03_2026/7e89_31012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e89_31012/03_2026/7e89_31012.cif" } resolution = 4.0 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= 0.002 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 96 5.16 5 C 14972 2.51 5 N 3988 2.21 5 O 4472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23528 Number of models: 1 Model: "" Number of chains: 4 Chain: "J" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "I" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "A" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "B" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Time building chain proxies: 5.17, per 1000 atoms: 0.22 Number of scatterers: 23528 At special positions: 0 Unit cell: (171, 161, 108, 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 96 16.00 O 4472 8.00 N 3988 7.00 C 14972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS J 349 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 465 " - pdb=" SG CYS J 468 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 492 " distance=2.03 Simple disulfide: pdb=" SG CYS J 673 " - pdb=" SG CYS J 784 " distance=2.03 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 356 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 468 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 492 " distance=2.03 Simple disulfide: pdb=" SG CYS I 673 " - pdb=" SG CYS I 784 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 784 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 465 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 673 " - pdb=" SG CYS B 784 " distance=2.03 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5488 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 54 sheets defined 17.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'J' and resid 70 through 76 removed outlier: 3.788A pdb=" N LEU J 74 " --> pdb=" O THR J 70 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE J 75 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 80 Processing helix chain 'J' and resid 118 through 122 removed outlier: 4.321A pdb=" N LYS J 121 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE J 122 " --> pdb=" O GLY J 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 118 through 122' Processing helix chain 'J' and resid 229 through 234 Processing helix chain 'J' and resid 517 through 527 Processing helix chain 'J' and resid 582 through 592 Processing helix chain 'J' and resid 607 through 613 Processing helix chain 'J' and resid 619 through 634 Processing helix chain 'J' and resid 650 through 659 removed outlier: 3.980A pdb=" N TYR J 654 " --> pdb=" O ASP J 650 " (cutoff:3.500A) Processing helix chain 'J' and resid 682 through 686 Processing helix chain 'J' and resid 687 through 696 removed outlier: 4.253A pdb=" N ARG J 693 " --> pdb=" O ALA J 689 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR J 694 " --> pdb=" O PHE J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 734 through 749 removed outlier: 4.263A pdb=" N THR J 738 " --> pdb=" O HIS J 734 " (cutoff:3.500A) Processing helix chain 'J' and resid 766 through 786 removed outlier: 3.705A pdb=" N GLU J 783 " --> pdb=" O ASN J 779 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS J 784 " --> pdb=" O PHE J 780 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG J 786 " --> pdb=" O VAL J 782 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 76 removed outlier: 3.607A pdb=" N LEU I 74 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 517 through 527 Processing helix chain 'I' and resid 582 through 591 Processing helix chain 'I' and resid 607 through 613 Processing helix chain 'I' and resid 619 through 635 Processing helix chain 'I' and resid 650 through 659 removed outlier: 3.643A pdb=" N TYR I 654 " --> pdb=" O ASP I 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 696 removed outlier: 3.921A pdb=" N ARG I 693 " --> pdb=" O ALA I 689 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR I 694 " --> pdb=" O PHE I 690 " (cutoff:3.500A) Processing helix chain 'I' and resid 710 through 715 removed outlier: 3.545A pdb=" N SER I 715 " --> pdb=" O ALA I 711 " (cutoff:3.500A) Processing helix chain 'I' and resid 734 through 749 removed outlier: 4.297A pdb=" N THR I 738 " --> pdb=" O HIS I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 785 removed outlier: 4.681A pdb=" N GLU I 783 " --> pdb=" O ASN I 779 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS I 784 " --> pdb=" O PHE I 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.788A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 118 through 122 removed outlier: 4.312A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 122 " --> pdb=" O GLY A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 122' Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 517 through 527 Processing helix chain 'A' and resid 582 through 592 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 619 through 634 Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.978A pdb=" N TYR A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 687 through 696 removed outlier: 4.253A pdb=" N ARG A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 694 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 749 removed outlier: 4.251A pdb=" N THR A 738 " --> pdb=" O HIS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 786 removed outlier: 3.744A pdb=" N GLU A 783 " --> pdb=" O ASN A 779 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 784 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 786 " --> pdb=" O VAL A 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.594A pdb=" N LEU B 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 517 through 527 Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 619 through 635 Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.634A pdb=" N TYR B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.935A pdb=" N ARG B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 694 " --> pdb=" O PHE B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 715 removed outlier: 3.541A pdb=" N SER B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 749 removed outlier: 4.304A pdb=" N THR B 738 " --> pdb=" O HIS B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 785 removed outlier: 4.646A pdb=" N GLU B 783 " --> pdb=" O ASN B 779 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS B 784 " --> pdb=" O PHE B 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 88 through 90 removed outlier: 3.535A pdb=" N SER J 90 " --> pdb=" O GLU J 93 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU J 93 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP J 106 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL J 103 " --> pdb=" O LEU J 116 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 112 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AA3, first strand: chain 'J' and resid 192 through 196 removed outlier: 6.095A pdb=" N TYR J 202 " --> pdb=" O ARG J 212 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG J 212 " --> pdb=" O TYR J 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'J' and resid 222 through 224 Processing sheet with id=AA6, first strand: chain 'J' and resid 264 through 266 Processing sheet with id=AA7, first strand: chain 'J' and resid 319 through 326 removed outlier: 5.596A pdb=" N ILE J 321 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU J 337 " --> pdb=" O ILE J 321 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET J 323 " --> pdb=" O THR J 335 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL J 343 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER J 344 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU J 361 " --> pdb=" O SER J 344 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU J 346 " --> pdb=" O LYS J 359 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL J 355 " --> pdb=" O ASP J 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 384 through 389 Processing sheet with id=AA9, first strand: chain 'J' and resid 425 through 432 removed outlier: 6.732A pdb=" N TYR J 439 " --> pdb=" O LEU J 429 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR J 431 " --> pdb=" O LYS J 437 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS J 437 " --> pdb=" O TYR J 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 478 through 481 removed outlier: 6.356A pdb=" N VAL J 502 " --> pdb=" O ASP J 513 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASP J 513 " --> pdb=" O VAL J 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 531 through 534 removed outlier: 3.795A pdb=" N LEU J 549 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL J 595 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS J 598 " --> pdb=" O VAL J 565 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR J 560 " --> pdb=" O ARG J 643 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ALA J 645 " --> pdb=" O TYR J 560 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU J 562 " --> pdb=" O ALA J 645 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE J 647 " --> pdb=" O LEU J 562 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU J 564 " --> pdb=" O PHE J 647 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS J 673 " --> pdb=" O VAL J 644 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL J 646 " --> pdb=" O CYS J 673 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY J 674 " --> pdb=" O GLN J 721 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 537 through 539 Processing sheet with id=AB4, first strand: chain 'J' and resid 725 through 727 removed outlier: 3.516A pdb=" N HIS J 726 " --> pdb=" O GLN J 755 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR J 757 " --> pdb=" O HIS J 726 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 88 through 90 removed outlier: 3.682A pdb=" N GLU I 93 " --> pdb=" O SER I 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 103 through 107 removed outlier: 6.716A pdb=" N VAL I 103 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AB8, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.821A pdb=" N TYR I 202 " --> pdb=" O ARG I 212 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG I 212 " --> pdb=" O TYR I 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AC1, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AC2, first strand: chain 'I' and resid 263 through 266 Processing sheet with id=AC3, first strand: chain 'I' and resid 319 through 326 removed outlier: 5.688A pdb=" N ILE I 321 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU I 337 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL I 343 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER I 344 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU I 361 " --> pdb=" O SER I 344 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU I 346 " --> pdb=" O LYS I 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 384 through 389 Processing sheet with id=AC5, first strand: chain 'I' and resid 425 through 432 removed outlier: 5.526A pdb=" N ILE I 428 " --> pdb=" O LEU I 441 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU I 441 " --> pdb=" O ILE I 428 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS I 437 " --> pdb=" O ASP I 432 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 478 through 481 removed outlier: 6.800A pdb=" N VAL I 502 " --> pdb=" O ASP I 513 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP I 513 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 531 through 532 removed outlier: 3.810A pdb=" N VAL I 595 " --> pdb=" O LEU I 549 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS I 598 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TYR I 560 " --> pdb=" O ARG I 643 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N ALA I 645 " --> pdb=" O TYR I 560 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU I 562 " --> pdb=" O ALA I 645 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE I 647 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU I 564 " --> pdb=" O PHE I 647 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 537 through 539 Processing sheet with id=AC9, first strand: chain 'I' and resid 722 through 727 removed outlier: 6.804A pdb=" N PHE I 722 " --> pdb=" O SER I 753 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLN I 755 " --> pdb=" O PHE I 722 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE I 724 " --> pdb=" O GLN I 755 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N TYR I 757 " --> pdb=" O ILE I 724 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS I 726 " --> pdb=" O TYR I 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.882A pdb=" N GLU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 106 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 103 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 112 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 129 through 132 Processing sheet with id=AD3, first strand: chain 'A' and resid 192 through 196 removed outlier: 6.092A pdb=" N TYR A 202 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG A 212 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AD5, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AD6, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AD7, first strand: chain 'A' and resid 319 through 326 removed outlier: 5.597A pdb=" N ILE A 321 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A 337 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 323 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 343 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A 344 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 361 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 346 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 355 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 384 through 389 Processing sheet with id=AD9, first strand: chain 'A' and resid 425 through 432 removed outlier: 6.736A pdb=" N TYR A 439 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N TYR A 431 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS A 437 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 478 through 481 removed outlier: 6.421A pdb=" N VAL A 502 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP A 513 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.769A pdb=" N LEU A 549 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 595 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS A 598 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N TYR A 560 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N ALA A 645 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 562 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE A 647 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 564 " --> pdb=" O PHE A 647 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 673 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 646 " --> pdb=" O CYS A 673 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 674 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AE4, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.519A pdb=" N HIS A 726 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 757 " --> pdb=" O HIS A 726 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.681A pdb=" N GLU B 93 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.717A pdb=" N VAL B 103 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 129 through 132 Processing sheet with id=AE8, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.825A pdb=" N TYR B 202 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG B 212 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 222 through 224 Processing sheet with id=AF1, first strand: chain 'B' and resid 222 through 224 Processing sheet with id=AF2, first strand: chain 'B' and resid 263 through 266 Processing sheet with id=AF3, first strand: chain 'B' and resid 319 through 326 removed outlier: 5.692A pdb=" N ILE B 321 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 337 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL B 343 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER B 344 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU B 361 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 346 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 384 through 389 Processing sheet with id=AF5, first strand: chain 'B' and resid 425 through 432 removed outlier: 5.489A pdb=" N ILE B 428 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 441 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS B 437 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 478 through 481 removed outlier: 6.797A pdb=" N VAL B 502 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP B 513 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.816A pdb=" N VAL B 595 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR B 560 " --> pdb=" O ARG B 643 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ALA B 645 " --> pdb=" O TYR B 560 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 562 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE B 647 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 564 " --> pdb=" O PHE B 647 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AF9, first strand: chain 'B' and resid 722 through 727 removed outlier: 6.793A pdb=" N PHE B 722 " --> pdb=" O SER B 753 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N GLN B 755 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE B 724 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N TYR B 757 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N HIS B 726 " --> pdb=" O TYR B 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 665 hydrogen bonds defined for protein. 1755 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: 5.14 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7640 1.34 - 1.46: 5798 1.46 - 1.58: 10538 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 24128 Sorted by residual: bond pdb=" C ILE I 162 " pdb=" N PRO I 163 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.43e+00 bond pdb=" C ILE B 162 " pdb=" N PRO B 163 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.34e+00 bond pdb=" C SER I 678 " pdb=" O SER I 678 " ideal model delta sigma weight residual 1.233 1.226 0.007 4.80e-03 4.34e+04 1.88e+00 bond pdb=" C ILE J 162 " pdb=" N PRO J 163 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 bond pdb=" C ILE A 162 " pdb=" N PRO A 163 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 ... (remaining 24123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 31862 1.70 - 3.39: 729 3.39 - 5.09: 104 5.09 - 6.78: 27 6.78 - 8.48: 2 Bond angle restraints: 32724 Sorted by residual: angle pdb=" C ILE I 659 " pdb=" N LEU I 660 " pdb=" CA LEU I 660 " ideal model delta sigma weight residual 123.21 117.95 5.26 1.19e+00 7.06e-01 1.96e+01 angle pdb=" C ILE B 659 " pdb=" N LEU B 660 " pdb=" CA LEU B 660 " ideal model delta sigma weight residual 123.21 118.10 5.11 1.19e+00 7.06e-01 1.85e+01 angle pdb=" N VAL J 710 " pdb=" CA VAL J 710 " pdb=" C VAL J 710 " ideal model delta sigma weight residual 112.98 108.96 4.02 1.25e+00 6.40e-01 1.04e+01 angle pdb=" N VAL A 710 " pdb=" CA VAL A 710 " pdb=" C VAL A 710 " ideal model delta sigma weight residual 112.98 108.96 4.02 1.25e+00 6.40e-01 1.03e+01 angle pdb=" N CYS J 468 " pdb=" CA CYS J 468 " pdb=" CB CYS J 468 " ideal model delta sigma weight residual 111.62 107.28 4.34 1.43e+00 4.89e-01 9.19e+00 ... (remaining 32719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12901 17.81 - 35.62: 1262 35.62 - 53.42: 220 53.42 - 71.23: 35 71.23 - 89.04: 26 Dihedral angle restraints: 14444 sinusoidal: 5888 harmonic: 8556 Sorted by residual: dihedral pdb=" CB CYS J 474 " pdb=" SG CYS J 474 " pdb=" SG CYS J 492 " pdb=" CB CYS J 492 " ideal model delta sinusoidal sigma weight residual -86.00 -23.15 -62.85 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 492 " pdb=" CB CYS A 492 " ideal model delta sinusoidal sigma weight residual -86.00 -23.26 -62.74 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS J 673 " pdb=" SG CYS J 673 " pdb=" SG CYS J 784 " pdb=" CB CYS J 784 " ideal model delta sinusoidal sigma weight residual 93.00 42.85 50.15 1 1.00e+01 1.00e-02 3.45e+01 ... (remaining 14441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2072 0.032 - 0.064: 952 0.064 - 0.096: 316 0.096 - 0.127: 177 0.127 - 0.159: 19 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CB ILE B 438 " pdb=" CA ILE B 438 " pdb=" CG1 ILE B 438 " pdb=" CG2 ILE B 438 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB ILE I 438 " pdb=" CA ILE I 438 " pdb=" CG1 ILE I 438 " pdb=" CG2 ILE I 438 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL B 158 " pdb=" N VAL B 158 " pdb=" C VAL B 158 " pdb=" CB VAL B 158 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 3533 not shown) Planarity restraints: 4216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 162 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 163 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 162 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO J 163 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO J 163 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 163 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 390 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO J 391 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 391 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 391 " -0.022 5.00e-02 4.00e+02 ... (remaining 4213 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1558 2.73 - 3.27: 25498 3.27 - 3.81: 40705 3.81 - 4.36: 49604 4.36 - 4.90: 82175 Nonbonded interactions: 199540 Sorted by model distance: nonbonded pdb=" O VAL A 69 " pdb=" OG SER A 590 " model vdw 2.182 3.040 nonbonded pdb=" O VAL J 69 " pdb=" OG SER J 590 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR B 475 " pdb=" OE1 GLU B 577 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR I 475 " pdb=" OE1 GLU I 577 " model vdw 2.195 3.040 nonbonded pdb=" OD2 ASP I 640 " pdb=" OG1 THR I 642 " model vdw 2.202 3.040 ... (remaining 199535 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 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.820 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24144 Z= 0.146 Angle : 0.626 8.475 32756 Z= 0.339 Chirality : 0.045 0.159 3536 Planarity : 0.004 0.042 4216 Dihedral : 14.518 89.041 8908 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.15), residues: 2908 helix: -0.64 (0.25), residues: 422 sheet: -0.87 (0.18), residues: 836 loop : -1.93 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 463 TYR 0.023 0.001 TYR I 686 PHE 0.018 0.002 PHE J 75 TRP 0.016 0.002 TRP A 229 HIS 0.005 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00318 (24128) covalent geometry : angle 0.62556 (32724) SS BOND : bond 0.00253 ( 16) SS BOND : angle 1.10229 ( 32) hydrogen bonds : bond 0.17653 ( 657) hydrogen bonds : angle 8.35299 ( 1755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ILE cc_start: 0.6301 (mm) cc_final: 0.5978 (mm) REVERT: J 117 ILE cc_start: 0.6027 (mm) cc_final: 0.5660 (mm) REVERT: J 129 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7617 (ttp-110) REVERT: J 309 MET cc_start: 0.7138 (tpt) cc_final: 0.6936 (tpp) REVERT: J 369 HIS cc_start: 0.6339 (t-170) cc_final: 0.6002 (t-170) REVERT: J 399 TYR cc_start: 0.4479 (m-80) cc_final: 0.4137 (m-80) REVERT: J 483 HIS cc_start: 0.4973 (m-70) cc_final: 0.4649 (m90) REVERT: J 485 MET cc_start: 0.4462 (mpp) cc_final: 0.4186 (mpp) REVERT: J 535 ARG cc_start: 0.6055 (ttm110) cc_final: 0.4861 (tmt-80) REVERT: J 594 VAL cc_start: 0.5820 (m) cc_final: 0.5602 (m) REVERT: J 595 VAL cc_start: 0.6885 (p) cc_final: 0.6630 (p) REVERT: J 630 VAL cc_start: 0.6698 (t) cc_final: 0.6430 (t) REVERT: J 673 CYS cc_start: 0.1887 (p) cc_final: 0.1667 (p) REVERT: J 685 LEU cc_start: 0.8253 (mt) cc_final: 0.7950 (mp) REVERT: J 703 ARG cc_start: 0.7115 (ttp-170) cc_final: 0.6772 (ttm170) REVERT: J 732 LYS cc_start: 0.8078 (tptp) cc_final: 0.7757 (mmtt) REVERT: J 744 GLN cc_start: 0.7658 (tp40) cc_final: 0.7309 (tm-30) REVERT: I 77 GLU cc_start: 0.7012 (tp30) cc_final: 0.6628 (mm-30) REVERT: I 164 HIS cc_start: 0.5613 (p-80) cc_final: 0.5328 (p90) REVERT: I 304 HIS cc_start: 0.5970 (t-170) cc_final: 0.5669 (t70) REVERT: I 308 MET cc_start: 0.8058 (mpp) cc_final: 0.7079 (mpp) REVERT: I 546 MET cc_start: 0.8112 (tmm) cc_final: 0.7762 (tmm) REVERT: I 657 THR cc_start: 0.8657 (p) cc_final: 0.8424 (p) REVERT: I 778 ILE cc_start: 0.8242 (mm) cc_final: 0.7986 (mm) REVERT: A 95 ILE cc_start: 0.6268 (mm) cc_final: 0.5942 (mm) REVERT: A 117 ILE cc_start: 0.6017 (mm) cc_final: 0.5652 (mm) REVERT: A 129 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7615 (ttp-110) REVERT: A 309 MET cc_start: 0.7125 (tpt) cc_final: 0.6923 (tpp) REVERT: A 369 HIS cc_start: 0.6338 (t-170) cc_final: 0.5969 (t-170) REVERT: A 399 TYR cc_start: 0.4481 (m-80) cc_final: 0.4121 (m-80) REVERT: A 483 HIS cc_start: 0.4977 (m-70) cc_final: 0.4592 (m90) REVERT: A 485 MET cc_start: 0.4756 (mpp) cc_final: 0.4311 (mpp) REVERT: A 535 ARG cc_start: 0.6111 (ttm110) cc_final: 0.4998 (tmt-80) REVERT: A 594 VAL cc_start: 0.5857 (m) cc_final: 0.5648 (p) REVERT: A 630 VAL cc_start: 0.6688 (t) cc_final: 0.6413 (t) REVERT: A 685 LEU cc_start: 0.8179 (mt) cc_final: 0.7853 (mp) REVERT: A 703 ARG cc_start: 0.7195 (ttp-170) cc_final: 0.6859 (ttm170) REVERT: A 732 LYS cc_start: 0.8070 (tptp) cc_final: 0.7758 (mmtt) REVERT: A 744 GLN cc_start: 0.7498 (tp40) cc_final: 0.7264 (tm-30) REVERT: B 77 GLU cc_start: 0.7029 (tp30) cc_final: 0.6641 (mm-30) REVERT: B 164 HIS cc_start: 0.5558 (p-80) cc_final: 0.5291 (p90) REVERT: B 308 MET cc_start: 0.8058 (mpp) cc_final: 0.7082 (mpp) REVERT: B 546 MET cc_start: 0.8198 (tmm) cc_final: 0.7881 (tmm) REVERT: B 657 THR cc_start: 0.8647 (p) cc_final: 0.8413 (p) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.1818 time to fit residues: 96.7265 Evaluate side-chains 186 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 0.0020 overall best weight: 3.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 190 GLN J 483 HIS J 504 ASN J 591 HIS I 144 ASN ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 451 GLN ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 483 HIS ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN B 483 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.082338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.067650 restraints weight = 109980.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.067951 restraints weight = 76432.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.068103 restraints weight = 78947.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.068505 restraints weight = 60239.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.068587 restraints weight = 54842.880| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24144 Z= 0.212 Angle : 0.706 7.672 32756 Z= 0.372 Chirality : 0.047 0.146 3536 Planarity : 0.005 0.044 4216 Dihedral : 5.436 32.160 3208 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 1.43 % Allowed : 9.75 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.15), residues: 2908 helix: -0.90 (0.24), residues: 442 sheet: -1.05 (0.18), residues: 830 loop : -1.99 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 615 TYR 0.018 0.002 TYR J 320 PHE 0.027 0.003 PHE A 722 TRP 0.017 0.002 TRP A 367 HIS 0.018 0.002 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00480 (24128) covalent geometry : angle 0.70501 (32724) SS BOND : bond 0.00825 ( 16) SS BOND : angle 1.20498 ( 32) hydrogen bonds : bond 0.05154 ( 657) hydrogen bonds : angle 6.91832 ( 1755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5686 (mm) cc_final: 0.5275 (mm) REVERT: J 323 MET cc_start: 0.5944 (tmm) cc_final: 0.4934 (tmm) REVERT: J 369 HIS cc_start: 0.6619 (t-170) cc_final: 0.5960 (t-170) REVERT: J 535 ARG cc_start: 0.5627 (ttm110) cc_final: 0.5373 (mtt180) REVERT: J 744 GLN cc_start: 0.7547 (tp40) cc_final: 0.7162 (tm-30) REVERT: I 77 GLU cc_start: 0.7266 (tp30) cc_final: 0.6760 (mm-30) REVERT: I 85 GLU cc_start: 0.7403 (tp30) cc_final: 0.7094 (tp30) REVERT: I 546 MET cc_start: 0.7737 (tmm) cc_final: 0.7367 (tmm) REVERT: I 562 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.6055 (tp) REVERT: I 627 MET cc_start: 0.7147 (tpt) cc_final: 0.6708 (ttp) REVERT: A 117 ILE cc_start: 0.5678 (mm) cc_final: 0.5257 (mm) REVERT: A 323 MET cc_start: 0.5963 (tmm) cc_final: 0.4942 (tmm) REVERT: A 369 HIS cc_start: 0.6622 (t-170) cc_final: 0.5954 (t-170) REVERT: A 535 ARG cc_start: 0.5690 (ttm110) cc_final: 0.4630 (tmt-80) REVERT: A 685 LEU cc_start: 0.7877 (mt) cc_final: 0.7596 (mp) REVERT: A 744 GLN cc_start: 0.7538 (tp40) cc_final: 0.7160 (tm-30) REVERT: B 77 GLU cc_start: 0.7270 (tp30) cc_final: 0.6782 (mm-30) REVERT: B 85 GLU cc_start: 0.7395 (tp30) cc_final: 0.7082 (tp30) REVERT: B 546 MET cc_start: 0.7805 (tmm) cc_final: 0.7191 (tmm) REVERT: B 562 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.6041 (tp) REVERT: B 627 MET cc_start: 0.7114 (tpt) cc_final: 0.6691 (ttp) outliers start: 37 outliers final: 27 residues processed: 223 average time/residue: 0.1533 time to fit residues: 54.4407 Evaluate side-chains 180 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 504 ASN Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain J residue 777 ILE Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 234 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 76 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 360 HIS J 504 ASN ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.082578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.067980 restraints weight = 110277.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.067570 restraints weight = 77443.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.068031 restraints weight = 73084.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.068157 restraints weight = 60949.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.068323 restraints weight = 58345.401| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24144 Z= 0.171 Angle : 0.645 7.940 32756 Z= 0.341 Chirality : 0.046 0.143 3536 Planarity : 0.005 0.045 4216 Dihedral : 5.346 33.380 3208 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.54 % Allowed : 12.90 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.15), residues: 2908 helix: -0.81 (0.23), residues: 454 sheet: -1.07 (0.18), residues: 808 loop : -2.09 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 641 TYR 0.038 0.002 TYR B 431 PHE 0.020 0.002 PHE I 722 TRP 0.034 0.002 TRP B 336 HIS 0.005 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00379 (24128) covalent geometry : angle 0.64525 (32724) SS BOND : bond 0.00471 ( 16) SS BOND : angle 0.75815 ( 32) hydrogen bonds : bond 0.04500 ( 657) hydrogen bonds : angle 6.58871 ( 1755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 109 GLU cc_start: 0.5743 (pt0) cc_final: 0.5511 (pt0) REVERT: J 117 ILE cc_start: 0.5474 (mm) cc_final: 0.5173 (mm) REVERT: J 323 MET cc_start: 0.6396 (tmm) cc_final: 0.5312 (tmm) REVERT: J 369 HIS cc_start: 0.6665 (t-170) cc_final: 0.5970 (t-170) REVERT: J 535 ARG cc_start: 0.5620 (ttm110) cc_final: 0.5371 (mtt180) REVERT: J 744 GLN cc_start: 0.7347 (tp40) cc_final: 0.7017 (tm-30) REVERT: I 87 LYS cc_start: 0.7960 (mttp) cc_final: 0.7727 (ptpp) REVERT: I 308 MET cc_start: 0.7831 (mpp) cc_final: 0.7427 (mpp) REVERT: I 546 MET cc_start: 0.7837 (tmm) cc_final: 0.7165 (tmm) REVERT: I 567 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8115 (t0) REVERT: I 627 MET cc_start: 0.7183 (tpt) cc_final: 0.6706 (ttp) REVERT: A 117 ILE cc_start: 0.5624 (mm) cc_final: 0.5326 (mm) REVERT: A 323 MET cc_start: 0.6349 (tmm) cc_final: 0.5200 (tmm) REVERT: A 369 HIS cc_start: 0.6666 (t-170) cc_final: 0.5967 (t-170) REVERT: A 535 ARG cc_start: 0.5743 (ttm110) cc_final: 0.5315 (mtt180) REVERT: A 744 GLN cc_start: 0.7412 (tp40) cc_final: 0.7076 (tm-30) REVERT: B 87 LYS cc_start: 0.7945 (mttp) cc_final: 0.7716 (ptpp) REVERT: B 308 MET cc_start: 0.7814 (mpp) cc_final: 0.7391 (mpp) REVERT: B 546 MET cc_start: 0.7873 (tmm) cc_final: 0.7198 (tmm) REVERT: B 567 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8122 (t0) REVERT: B 627 MET cc_start: 0.7139 (tpt) cc_final: 0.6685 (ttp) outliers start: 66 outliers final: 39 residues processed: 234 average time/residue: 0.1474 time to fit residues: 56.4336 Evaluate side-chains 191 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 630 VAL Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 0.0970 chunk 51 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 273 optimal weight: 0.2980 chunk 238 optimal weight: 0.0070 chunk 252 optimal weight: 20.0000 overall best weight: 3.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 ASN ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.082534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.067773 restraints weight = 110238.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.067897 restraints weight = 76788.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.068162 restraints weight = 76550.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.068483 restraints weight = 59886.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.068588 restraints weight = 55323.132| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24144 Z= 0.178 Angle : 0.659 8.473 32756 Z= 0.349 Chirality : 0.046 0.200 3536 Planarity : 0.005 0.047 4216 Dihedral : 5.449 35.862 3208 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 3.08 % Allowed : 15.02 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.15), residues: 2908 helix: -0.71 (0.23), residues: 442 sheet: -1.17 (0.18), residues: 800 loop : -2.16 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 450 TYR 0.015 0.002 TYR I 431 PHE 0.024 0.002 PHE I 722 TRP 0.032 0.002 TRP I 336 HIS 0.006 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00401 (24128) covalent geometry : angle 0.65915 (32724) SS BOND : bond 0.00416 ( 16) SS BOND : angle 0.80030 ( 32) hydrogen bonds : bond 0.04361 ( 657) hydrogen bonds : angle 6.45689 ( 1755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 164 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 109 GLU cc_start: 0.5913 (pt0) cc_final: 0.5699 (pt0) REVERT: J 117 ILE cc_start: 0.5521 (mm) cc_final: 0.5239 (mm) REVERT: J 218 LYS cc_start: 0.7509 (ptmt) cc_final: 0.7211 (ptpt) REVERT: J 323 MET cc_start: 0.6348 (tmm) cc_final: 0.5779 (tmm) REVERT: J 369 HIS cc_start: 0.6864 (t-170) cc_final: 0.6220 (t-170) REVERT: J 387 ILE cc_start: 0.4126 (OUTLIER) cc_final: 0.3739 (mt) REVERT: J 535 ARG cc_start: 0.5559 (ttm110) cc_final: 0.4346 (tmt-80) REVERT: J 744 GLN cc_start: 0.7196 (tp40) cc_final: 0.6914 (tm-30) REVERT: I 143 TYR cc_start: 0.5432 (p90) cc_final: 0.4922 (p90) REVERT: I 308 MET cc_start: 0.7732 (mpp) cc_final: 0.7258 (mpp) REVERT: I 316 MET cc_start: 0.5842 (tpt) cc_final: 0.5427 (tpt) REVERT: I 562 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5790 (tp) REVERT: I 567 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8038 (t0) REVERT: I 627 MET cc_start: 0.7233 (tpt) cc_final: 0.6728 (ttp) REVERT: I 657 THR cc_start: 0.8587 (p) cc_final: 0.8321 (p) REVERT: A 117 ILE cc_start: 0.5514 (mm) cc_final: 0.5247 (mm) REVERT: A 218 LYS cc_start: 0.7570 (ptmt) cc_final: 0.7255 (ptpt) REVERT: A 323 MET cc_start: 0.6270 (tmm) cc_final: 0.5706 (tmm) REVERT: A 369 HIS cc_start: 0.6897 (t-170) cc_final: 0.6271 (t-170) REVERT: A 387 ILE cc_start: 0.3975 (OUTLIER) cc_final: 0.3562 (mt) REVERT: A 744 GLN cc_start: 0.7262 (tp40) cc_final: 0.6957 (tm-30) REVERT: B 143 TYR cc_start: 0.5506 (p90) cc_final: 0.4995 (p90) REVERT: B 308 MET cc_start: 0.7703 (mpp) cc_final: 0.7235 (mpp) REVERT: B 316 MET cc_start: 0.5842 (tpt) cc_final: 0.5426 (tpt) REVERT: B 424 ASP cc_start: 0.5857 (m-30) cc_final: 0.5616 (m-30) REVERT: B 562 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5730 (tp) REVERT: B 567 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 627 MET cc_start: 0.7189 (tpt) cc_final: 0.6705 (ttp) REVERT: B 657 THR cc_start: 0.8559 (p) cc_final: 0.8290 (p) outliers start: 80 outliers final: 46 residues processed: 233 average time/residue: 0.1402 time to fit residues: 54.1828 Evaluate side-chains 205 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 95 optimal weight: 0.3980 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.082594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.067961 restraints weight = 110290.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.067522 restraints weight = 81104.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.068093 restraints weight = 79818.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.068164 restraints weight = 66095.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.068235 restraints weight = 61855.011| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24144 Z= 0.181 Angle : 0.661 8.479 32756 Z= 0.350 Chirality : 0.046 0.176 3536 Planarity : 0.005 0.052 4216 Dihedral : 5.511 38.632 3208 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 3.93 % Allowed : 16.56 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.14), residues: 2908 helix: -0.67 (0.23), residues: 434 sheet: -1.16 (0.18), residues: 800 loop : -2.22 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 136 TYR 0.015 0.002 TYR I 253 PHE 0.021 0.002 PHE I 722 TRP 0.024 0.002 TRP A 367 HIS 0.006 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00412 (24128) covalent geometry : angle 0.66093 (32724) SS BOND : bond 0.00412 ( 16) SS BOND : angle 0.87380 ( 32) hydrogen bonds : bond 0.04189 ( 657) hydrogen bonds : angle 6.35850 ( 1755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 167 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 323 MET cc_start: 0.6331 (tmm) cc_final: 0.5782 (tmm) REVERT: J 369 HIS cc_start: 0.6828 (t-170) cc_final: 0.6300 (t-170) REVERT: J 387 ILE cc_start: 0.4153 (OUTLIER) cc_final: 0.3754 (mt) REVERT: J 744 GLN cc_start: 0.7094 (tp40) cc_final: 0.6850 (tm-30) REVERT: I 143 TYR cc_start: 0.5604 (p90) cc_final: 0.5086 (p90) REVERT: I 308 MET cc_start: 0.7729 (mpp) cc_final: 0.7381 (mpp) REVERT: I 316 MET cc_start: 0.5848 (tpt) cc_final: 0.5472 (tpt) REVERT: I 546 MET cc_start: 0.7717 (tmm) cc_final: 0.7259 (tmm) REVERT: I 562 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5701 (tp) REVERT: I 567 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8058 (t0) REVERT: I 627 MET cc_start: 0.7014 (tpt) cc_final: 0.6603 (ttp) REVERT: I 657 THR cc_start: 0.8498 (p) cc_final: 0.8239 (p) REVERT: A 130 TYR cc_start: 0.4987 (p90) cc_final: 0.4638 (p90) REVERT: A 323 MET cc_start: 0.6289 (tmm) cc_final: 0.5671 (tmm) REVERT: A 369 HIS cc_start: 0.6834 (t-170) cc_final: 0.6272 (t-170) REVERT: A 387 ILE cc_start: 0.4166 (OUTLIER) cc_final: 0.3648 (mt) REVERT: B 143 TYR cc_start: 0.5634 (p90) cc_final: 0.5123 (p90) REVERT: B 308 MET cc_start: 0.7714 (mpp) cc_final: 0.7356 (mpp) REVERT: B 316 MET cc_start: 0.5841 (tpt) cc_final: 0.5462 (tpt) REVERT: B 424 ASP cc_start: 0.6093 (m-30) cc_final: 0.5777 (m-30) REVERT: B 562 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5665 (tp) REVERT: B 567 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8028 (t0) REVERT: B 627 MET cc_start: 0.6991 (tpt) cc_final: 0.6601 (ttp) REVERT: B 657 THR cc_start: 0.8463 (p) cc_final: 0.8199 (p) outliers start: 102 outliers final: 53 residues processed: 261 average time/residue: 0.1342 time to fit residues: 59.3514 Evaluate side-chains 210 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 118 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 0.2980 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 151 HIS ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 606 GLN I 744 GLN ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.082320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.067812 restraints weight = 111794.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.067760 restraints weight = 82862.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.068051 restraints weight = 85885.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.068416 restraints weight = 64860.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.068632 restraints weight = 59501.088| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24144 Z= 0.216 Angle : 0.719 9.306 32756 Z= 0.378 Chirality : 0.047 0.178 3536 Planarity : 0.005 0.060 4216 Dihedral : 5.758 41.087 3208 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 4.01 % Allowed : 18.07 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.14), residues: 2908 helix: -1.00 (0.22), residues: 446 sheet: -1.27 (0.18), residues: 818 loop : -2.22 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.018 0.002 TYR I 253 PHE 0.025 0.003 PHE I 722 TRP 0.026 0.002 TRP J 367 HIS 0.007 0.002 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00490 (24128) covalent geometry : angle 0.71808 (32724) SS BOND : bond 0.00436 ( 16) SS BOND : angle 1.09925 ( 32) hydrogen bonds : bond 0.04412 ( 657) hydrogen bonds : angle 6.51370 ( 1755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 154 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5343 (mm) cc_final: 0.4972 (mm) REVERT: J 126 ARG cc_start: 0.7372 (tpm170) cc_final: 0.6825 (mtm-85) REVERT: J 323 MET cc_start: 0.6217 (tmm) cc_final: 0.5653 (tmm) REVERT: J 369 HIS cc_start: 0.6848 (t-170) cc_final: 0.6184 (t-170) REVERT: J 387 ILE cc_start: 0.4067 (OUTLIER) cc_final: 0.3600 (mt) REVERT: I 59 GLU cc_start: 0.1033 (OUTLIER) cc_final: 0.0703 (pt0) REVERT: I 143 TYR cc_start: 0.5833 (p90) cc_final: 0.5348 (p90) REVERT: I 308 MET cc_start: 0.7654 (mpp) cc_final: 0.7379 (mpp) REVERT: I 316 MET cc_start: 0.5859 (tpt) cc_final: 0.5471 (tpt) REVERT: I 562 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5752 (tp) REVERT: I 567 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8003 (t0) REVERT: I 627 MET cc_start: 0.7120 (tpt) cc_final: 0.6688 (ttp) REVERT: I 657 THR cc_start: 0.8574 (p) cc_final: 0.8334 (p) REVERT: I 698 HIS cc_start: 0.5720 (OUTLIER) cc_final: 0.5061 (t70) REVERT: A 117 ILE cc_start: 0.5336 (mm) cc_final: 0.4966 (mm) REVERT: A 323 MET cc_start: 0.6267 (tmm) cc_final: 0.5095 (tmm) REVERT: A 369 HIS cc_start: 0.6819 (t-170) cc_final: 0.6115 (t-170) REVERT: A 387 ILE cc_start: 0.3964 (OUTLIER) cc_final: 0.3360 (mt) REVERT: A 783 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: B 59 GLU cc_start: 0.1007 (OUTLIER) cc_final: 0.0692 (pt0) REVERT: B 143 TYR cc_start: 0.5845 (p90) cc_final: 0.5367 (p90) REVERT: B 308 MET cc_start: 0.7637 (mpp) cc_final: 0.7346 (mpp) REVERT: B 316 MET cc_start: 0.5813 (tpt) cc_final: 0.5428 (tpt) REVERT: B 562 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5818 (tp) REVERT: B 567 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8022 (t0) REVERT: B 627 MET cc_start: 0.7057 (tpt) cc_final: 0.6800 (ttp) REVERT: B 657 THR cc_start: 0.8561 (p) cc_final: 0.8307 (p) REVERT: B 698 HIS cc_start: 0.5707 (OUTLIER) cc_final: 0.4972 (t70) outliers start: 104 outliers final: 57 residues processed: 250 average time/residue: 0.1370 time to fit residues: 57.5909 Evaluate side-chains 212 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 144 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 511 MET Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 725 ILE Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 133 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 275 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 473 ASN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.083408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.068387 restraints weight = 110299.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.068254 restraints weight = 81406.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.068787 restraints weight = 70834.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.068928 restraints weight = 60974.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.069100 restraints weight = 57249.782| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24144 Z= 0.146 Angle : 0.656 9.087 32756 Z= 0.342 Chirality : 0.046 0.184 3536 Planarity : 0.004 0.046 4216 Dihedral : 5.501 37.491 3208 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.12 % Allowed : 19.30 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.15), residues: 2908 helix: -0.76 (0.23), residues: 446 sheet: -1.16 (0.18), residues: 828 loop : -2.16 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.019 0.002 TYR I 431 PHE 0.024 0.002 PHE B 377 TRP 0.032 0.002 TRP A 367 HIS 0.007 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00335 (24128) covalent geometry : angle 0.65478 (32724) SS BOND : bond 0.00261 ( 16) SS BOND : angle 1.35936 ( 32) hydrogen bonds : bond 0.03928 ( 657) hydrogen bonds : angle 6.21464 ( 1755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 169 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5273 (mm) cc_final: 0.4891 (mm) REVERT: J 126 ARG cc_start: 0.7279 (tpm170) cc_final: 0.6734 (mtm-85) REVERT: J 323 MET cc_start: 0.6270 (tmm) cc_final: 0.5639 (tmm) REVERT: J 369 HIS cc_start: 0.6795 (t-170) cc_final: 0.6113 (t-170) REVERT: J 387 ILE cc_start: 0.4063 (OUTLIER) cc_final: 0.3631 (mt) REVERT: J 783 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: I 143 TYR cc_start: 0.5774 (p90) cc_final: 0.5339 (p90) REVERT: I 308 MET cc_start: 0.7603 (mpp) cc_final: 0.7343 (mpp) REVERT: I 316 MET cc_start: 0.5751 (tpt) cc_final: 0.5339 (tpt) REVERT: I 485 MET cc_start: 0.4260 (mtt) cc_final: 0.4003 (mtt) REVERT: I 546 MET cc_start: 0.7681 (tmm) cc_final: 0.7359 (tmm) REVERT: I 567 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (t0) REVERT: I 627 MET cc_start: 0.7056 (tpt) cc_final: 0.6643 (ttp) REVERT: I 657 THR cc_start: 0.8460 (p) cc_final: 0.8197 (p) REVERT: I 698 HIS cc_start: 0.5752 (OUTLIER) cc_final: 0.5102 (t70) REVERT: A 117 ILE cc_start: 0.5229 (mm) cc_final: 0.4850 (mm) REVERT: A 323 MET cc_start: 0.6267 (tmm) cc_final: 0.5604 (tmm) REVERT: A 369 HIS cc_start: 0.6842 (t-170) cc_final: 0.6102 (t-170) REVERT: A 387 ILE cc_start: 0.4083 (OUTLIER) cc_final: 0.3612 (mt) REVERT: B 143 TYR cc_start: 0.5724 (p90) cc_final: 0.5284 (p90) REVERT: B 308 MET cc_start: 0.7596 (mpp) cc_final: 0.7339 (mpp) REVERT: B 316 MET cc_start: 0.5761 (tpt) cc_final: 0.5353 (tpt) REVERT: B 424 ASP cc_start: 0.6234 (m-30) cc_final: 0.5900 (m-30) REVERT: B 431 TYR cc_start: 0.3581 (t80) cc_final: 0.3281 (t80) REVERT: B 567 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8033 (t0) REVERT: B 627 MET cc_start: 0.7201 (tpt) cc_final: 0.6682 (ttp) REVERT: B 657 THR cc_start: 0.8452 (p) cc_final: 0.8174 (p) REVERT: B 698 HIS cc_start: 0.5746 (OUTLIER) cc_final: 0.4982 (t70) outliers start: 81 outliers final: 58 residues processed: 243 average time/residue: 0.1374 time to fit residues: 55.6364 Evaluate side-chains 220 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain J residue 783 GLU Chi-restraints excluded: chain I residue 82 HIS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 165 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 52 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.083046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.068629 restraints weight = 111578.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.067587 restraints weight = 84491.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.068085 restraints weight = 73730.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.068840 restraints weight = 62758.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.068816 restraints weight = 55345.132| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24144 Z= 0.169 Angle : 0.666 11.017 32756 Z= 0.349 Chirality : 0.046 0.178 3536 Planarity : 0.004 0.047 4216 Dihedral : 5.527 37.631 3208 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 3.24 % Allowed : 19.53 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 2908 helix: -0.59 (0.23), residues: 434 sheet: -1.08 (0.18), residues: 806 loop : -2.20 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 535 TYR 0.016 0.002 TYR J 763 PHE 0.031 0.002 PHE B 377 TRP 0.027 0.002 TRP A 367 HIS 0.006 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00384 (24128) covalent geometry : angle 0.66259 (32724) SS BOND : bond 0.00315 ( 16) SS BOND : angle 2.24135 ( 32) hydrogen bonds : bond 0.04027 ( 657) hydrogen bonds : angle 6.19846 ( 1755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 156 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5346 (mm) cc_final: 0.4961 (mm) REVERT: J 126 ARG cc_start: 0.7346 (tpm170) cc_final: 0.6774 (mtm-85) REVERT: J 323 MET cc_start: 0.6276 (tmm) cc_final: 0.5630 (tmm) REVERT: J 369 HIS cc_start: 0.6833 (t-170) cc_final: 0.6144 (t-170) REVERT: J 387 ILE cc_start: 0.4129 (OUTLIER) cc_final: 0.3680 (mt) REVERT: J 783 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: I 143 TYR cc_start: 0.5912 (p90) cc_final: 0.5469 (p90) REVERT: I 308 MET cc_start: 0.7603 (mpp) cc_final: 0.7337 (mpp) REVERT: I 316 MET cc_start: 0.5798 (tpt) cc_final: 0.5373 (tpt) REVERT: I 485 MET cc_start: 0.4366 (mtt) cc_final: 0.4072 (mtt) REVERT: I 546 MET cc_start: 0.7769 (tmm) cc_final: 0.7199 (tmm) REVERT: I 562 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5796 (tp) REVERT: I 627 MET cc_start: 0.7148 (tpt) cc_final: 0.6812 (ttp) REVERT: I 657 THR cc_start: 0.8510 (p) cc_final: 0.8241 (p) REVERT: I 698 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.5009 (t70) REVERT: A 117 ILE cc_start: 0.5321 (mm) cc_final: 0.4942 (mm) REVERT: A 126 ARG cc_start: 0.7315 (tpm170) cc_final: 0.6718 (mtm-85) REVERT: A 323 MET cc_start: 0.6269 (tmm) cc_final: 0.5617 (tmm) REVERT: A 369 HIS cc_start: 0.6836 (t-170) cc_final: 0.6151 (t-170) REVERT: A 387 ILE cc_start: 0.4132 (OUTLIER) cc_final: 0.3667 (mt) REVERT: A 783 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5470 (mp0) REVERT: B 143 TYR cc_start: 0.5939 (p90) cc_final: 0.5498 (p90) REVERT: B 308 MET cc_start: 0.7673 (mpp) cc_final: 0.7369 (mpp) REVERT: B 316 MET cc_start: 0.5781 (tpt) cc_final: 0.5353 (tpt) REVERT: B 424 ASP cc_start: 0.6237 (m-30) cc_final: 0.5812 (m-30) REVERT: B 485 MET cc_start: 0.4426 (mtt) cc_final: 0.4134 (mtt) REVERT: B 567 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8056 (t0) REVERT: B 627 MET cc_start: 0.7252 (tpt) cc_final: 0.6807 (ttp) REVERT: B 657 THR cc_start: 0.8492 (p) cc_final: 0.8236 (p) REVERT: B 698 HIS cc_start: 0.5858 (OUTLIER) cc_final: 0.5136 (t70) outliers start: 84 outliers final: 61 residues processed: 235 average time/residue: 0.1454 time to fit residues: 55.7544 Evaluate side-chains 219 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 150 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain J residue 783 GLU Chi-restraints excluded: chain I residue 82 HIS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 278 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 547 GLN ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.082669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.067957 restraints weight = 111726.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.067428 restraints weight = 81019.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.068018 restraints weight = 76758.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.068156 restraints weight = 62796.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.068227 restraints weight = 61570.821| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24144 Z= 0.195 Angle : 0.694 9.192 32756 Z= 0.366 Chirality : 0.046 0.177 3536 Planarity : 0.005 0.046 4216 Dihedral : 5.722 40.314 3208 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 3.12 % Allowed : 19.76 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 2908 helix: -0.91 (0.23), residues: 448 sheet: -1.19 (0.18), residues: 816 loop : -2.27 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 527 TYR 0.016 0.002 TYR I 253 PHE 0.021 0.002 PHE B 377 TRP 0.027 0.002 TRP A 367 HIS 0.011 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00443 (24128) covalent geometry : angle 0.69236 (32724) SS BOND : bond 0.00403 ( 16) SS BOND : angle 1.77963 ( 32) hydrogen bonds : bond 0.04181 ( 657) hydrogen bonds : angle 6.33580 ( 1755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 151 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5515 (mm) cc_final: 0.5093 (mm) REVERT: J 126 ARG cc_start: 0.7504 (tpm170) cc_final: 0.6840 (mtm-85) REVERT: J 323 MET cc_start: 0.6318 (tmm) cc_final: 0.5122 (tmm) REVERT: J 369 HIS cc_start: 0.6838 (t-170) cc_final: 0.6115 (t-170) REVERT: J 387 ILE cc_start: 0.3919 (OUTLIER) cc_final: 0.3462 (mt) REVERT: J 783 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6134 (mp0) REVERT: I 143 TYR cc_start: 0.5884 (p90) cc_final: 0.5463 (p90) REVERT: I 308 MET cc_start: 0.7632 (mpp) cc_final: 0.7338 (mpp) REVERT: I 316 MET cc_start: 0.5776 (tpt) cc_final: 0.5370 (tpt) REVERT: I 485 MET cc_start: 0.4546 (mtt) cc_final: 0.4231 (mtt) REVERT: I 562 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5785 (tp) REVERT: I 567 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8069 (t0) REVERT: I 627 MET cc_start: 0.7333 (tpt) cc_final: 0.6822 (ttp) REVERT: I 657 THR cc_start: 0.8532 (p) cc_final: 0.8284 (p) REVERT: I 698 HIS cc_start: 0.5857 (OUTLIER) cc_final: 0.5058 (t70) REVERT: A 117 ILE cc_start: 0.5425 (mm) cc_final: 0.4998 (mm) REVERT: A 126 ARG cc_start: 0.7484 (tpm170) cc_final: 0.6802 (mtm-85) REVERT: A 323 MET cc_start: 0.6314 (tmm) cc_final: 0.5666 (tmm) REVERT: A 369 HIS cc_start: 0.6852 (t-170) cc_final: 0.6132 (t-170) REVERT: A 387 ILE cc_start: 0.3930 (OUTLIER) cc_final: 0.3455 (mt) REVERT: A 783 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.5445 (mp0) REVERT: B 143 TYR cc_start: 0.5904 (p90) cc_final: 0.5442 (p90) REVERT: B 308 MET cc_start: 0.7609 (mpp) cc_final: 0.7334 (mpp) REVERT: B 316 MET cc_start: 0.5769 (tpt) cc_final: 0.5368 (tpt) REVERT: B 485 MET cc_start: 0.4501 (mtt) cc_final: 0.4172 (mtt) REVERT: B 562 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5826 (tp) REVERT: B 567 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8033 (t0) REVERT: B 627 MET cc_start: 0.7258 (tpt) cc_final: 0.6808 (ttp) REVERT: B 657 THR cc_start: 0.8531 (p) cc_final: 0.8285 (p) REVERT: B 698 HIS cc_start: 0.5869 (OUTLIER) cc_final: 0.5075 (t70) outliers start: 81 outliers final: 63 residues processed: 224 average time/residue: 0.1427 time to fit residues: 52.9526 Evaluate side-chains 218 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 145 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 504 ASN Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 511 MET Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain J residue 783 GLU Chi-restraints excluded: chain I residue 82 HIS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 201 optimal weight: 9.9990 chunk 185 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 209 optimal weight: 0.0270 chunk 73 optimal weight: 5.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 547 GLN I 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.084389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.069218 restraints weight = 109815.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.069077 restraints weight = 83625.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.069385 restraints weight = 66634.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.069537 restraints weight = 60221.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.069670 restraints weight = 56793.252| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24144 Z= 0.124 Angle : 0.627 10.516 32756 Z= 0.326 Chirality : 0.045 0.157 3536 Planarity : 0.004 0.040 4216 Dihedral : 5.291 33.633 3208 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 1.81 % Allowed : 21.11 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.15), residues: 2908 helix: -0.40 (0.24), residues: 436 sheet: -1.02 (0.19), residues: 788 loop : -2.09 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 535 TYR 0.014 0.001 TYR A 763 PHE 0.022 0.002 PHE B 377 TRP 0.026 0.002 TRP A 367 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00280 (24128) covalent geometry : angle 0.62704 (32724) SS BOND : bond 0.00245 ( 16) SS BOND : angle 0.90118 ( 32) hydrogen bonds : bond 0.03667 ( 657) hydrogen bonds : angle 5.91481 ( 1755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5325 (mm) cc_final: 0.4922 (mm) REVERT: J 126 ARG cc_start: 0.7349 (tpm170) cc_final: 0.6724 (mtm-85) REVERT: J 130 TYR cc_start: 0.5029 (p90) cc_final: 0.4757 (p90) REVERT: J 323 MET cc_start: 0.6295 (tmm) cc_final: 0.5627 (tmm) REVERT: J 369 HIS cc_start: 0.6900 (t-170) cc_final: 0.6158 (t-170) REVERT: J 783 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6052 (mp0) REVERT: I 143 TYR cc_start: 0.5782 (p90) cc_final: 0.5403 (p90) REVERT: I 308 MET cc_start: 0.7611 (mpp) cc_final: 0.7362 (mpp) REVERT: I 316 MET cc_start: 0.5628 (tpt) cc_final: 0.5233 (tpt) REVERT: I 567 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7910 (t0) REVERT: I 627 MET cc_start: 0.7262 (tpt) cc_final: 0.6790 (ttp) REVERT: I 657 THR cc_start: 0.8476 (p) cc_final: 0.8218 (p) REVERT: I 698 HIS cc_start: 0.5814 (OUTLIER) cc_final: 0.5178 (t70) REVERT: A 117 ILE cc_start: 0.5607 (mm) cc_final: 0.5205 (mm) REVERT: A 126 ARG cc_start: 0.7351 (tpm170) cc_final: 0.6699 (mtm-85) REVERT: A 323 MET cc_start: 0.6310 (tmm) cc_final: 0.5630 (tmm) REVERT: A 369 HIS cc_start: 0.6895 (t-170) cc_final: 0.6161 (t-170) REVERT: B 143 TYR cc_start: 0.5815 (p90) cc_final: 0.5433 (p90) REVERT: B 308 MET cc_start: 0.7624 (mpp) cc_final: 0.7371 (mpp) REVERT: B 316 MET cc_start: 0.5734 (tpt) cc_final: 0.5336 (tpt) REVERT: B 424 ASP cc_start: 0.6380 (m-30) cc_final: 0.6019 (m-30) REVERT: B 627 MET cc_start: 0.7055 (tpt) cc_final: 0.6690 (ttp) REVERT: B 657 THR cc_start: 0.8441 (p) cc_final: 0.8163 (p) outliers start: 47 outliers final: 39 residues processed: 219 average time/residue: 0.1475 time to fit residues: 52.5947 Evaluate side-chains 201 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 504 ASN Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 783 GLU Chi-restraints excluded: chain I residue 82 HIS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 183 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 547 GLN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.082341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.067917 restraints weight = 111671.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.067454 restraints weight = 83515.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.067991 restraints weight = 78255.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.068193 restraints weight = 64602.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.068328 restraints weight = 59620.236| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24144 Z= 0.237 Angle : 0.742 9.705 32756 Z= 0.391 Chirality : 0.049 0.421 3536 Planarity : 0.005 0.048 4216 Dihedral : 5.840 41.695 3208 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.07 % Favored : 88.86 % Rotamer: Outliers : 2.66 % Allowed : 20.57 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.14), residues: 2908 helix: -0.97 (0.23), residues: 448 sheet: -1.42 (0.18), residues: 806 loop : -2.22 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 129 TYR 0.043 0.002 TYR J 453 PHE 0.025 0.003 PHE I 512 TRP 0.024 0.002 TRP A 367 HIS 0.016 0.002 HIS J 772 Details of bonding type rmsd covalent geometry : bond 0.00537 (24128) covalent geometry : angle 0.74142 (32724) SS BOND : bond 0.00354 ( 16) SS BOND : angle 0.90567 ( 32) hydrogen bonds : bond 0.04436 ( 657) hydrogen bonds : angle 6.39879 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3154.64 seconds wall clock time: 56 minutes 6.33 seconds (3366.33 seconds total)