Starting phenix.real_space_refine on Sat Jul 4 21:02:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8g_31018/07_2026/7e8g_31018.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8g_31018/07_2026/7e8g_31018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e8g_31018/07_2026/7e8g_31018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8g_31018/07_2026/7e8g_31018.map" model { file = "/net/cci-nas-00/data/ceres_data/7e8g_31018/07_2026/7e8g_31018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8g_31018/07_2026/7e8g_31018.cif" } resolution = 4.5 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 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: "L" 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: "K" 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: 5.67, per 1000 atoms: 0.24 Number of scatterers: 23528 At special positions: 0 Unit cell: (161.431, 215.576, 106.284, 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 L 349 " - pdb=" SG CYS L 356 " distance=2.03 Simple disulfide: pdb=" SG CYS L 465 " - pdb=" SG CYS L 468 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 492 " distance=2.03 Simple disulfide: pdb=" SG CYS L 673 " - pdb=" SG CYS L 784 " distance=2.03 Simple disulfide: pdb=" SG CYS K 349 " - pdb=" SG CYS K 356 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 492 " distance=2.03 Simple disulfide: pdb=" SG CYS K 673 " - pdb=" SG CYS K 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: 1.84 Conformation dependent library (CDL) restraints added in 678.7 milliseconds 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: 53 helices and 46 sheets defined 17.7% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'J' and resid 70 through 75 Processing helix chain 'J' and resid 76 through 80 Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 517 through 527 Processing helix chain 'J' and resid 582 through 591 Processing helix chain 'J' and resid 607 through 614 removed outlier: 4.427A pdb=" N VAL J 614 " --> pdb=" O LEU J 610 " (cutoff:3.500A) Processing helix chain 'J' and resid 621 through 635 Processing helix chain 'J' and resid 649 through 658 Processing helix chain 'J' and resid 682 through 686 Processing helix chain 'J' and resid 687 through 696 removed outlier: 4.351A pdb=" N ARG J 693 " --> pdb=" O ALA J 689 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR J 694 " --> pdb=" O PHE J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 705 through 709 removed outlier: 3.907A pdb=" N LYS J 709 " --> pdb=" O GLU J 706 " (cutoff:3.500A) Processing helix chain 'J' and resid 710 through 715 removed outlier: 3.755A pdb=" N SER J 715 " --> pdb=" O HIS J 712 " (cutoff:3.500A) Processing helix chain 'J' and resid 734 through 749 removed outlier: 4.144A pdb=" N THR J 738 " --> pdb=" O HIS J 734 " (cutoff:3.500A) Processing helix chain 'J' and resid 766 through 784 removed outlier: 3.763A pdb=" N GLU J 783 " --> pdb=" O ASN J 779 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS J 784 " --> pdb=" O PHE J 780 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 75 removed outlier: 3.875A pdb=" N LEU I 74 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE I 75 " --> pdb=" O VAL I 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 70 through 75' Processing helix chain 'I' and resid 118 through 123 removed outlier: 3.872A pdb=" N LYS I 121 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE I 122 " --> pdb=" O GLY I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 517 through 527 removed outlier: 3.731A pdb=" N ARG I 527 " --> pdb=" O ALA I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 582 through 590 Processing helix chain 'I' and resid 607 through 614 removed outlier: 4.597A pdb=" N VAL I 614 " --> pdb=" O LEU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 635 Processing helix chain 'I' and resid 649 through 658 removed outlier: 3.613A pdb=" N TYR I 654 " --> pdb=" O ASP I 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 682 through 686 Processing helix chain 'I' and resid 687 through 696 removed outlier: 3.810A pdb=" N ARG I 693 " --> pdb=" O ALA I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 714 removed outlier: 3.566A pdb=" N HIS I 712 " --> pdb=" O LYS I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 734 through 748 removed outlier: 4.390A pdb=" N THR I 738 " --> pdb=" O HIS I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 786 removed outlier: 3.573A pdb=" N CYS I 784 " --> pdb=" O PHE I 780 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 Processing helix chain 'L' and resid 76 through 80 Processing helix chain 'L' and resid 228 through 234 Processing helix chain 'L' and resid 517 through 527 Processing helix chain 'L' and resid 582 through 592 Processing helix chain 'L' and resid 607 through 614 removed outlier: 4.435A pdb=" N VAL L 614 " --> pdb=" O LEU L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 621 through 635 Processing helix chain 'L' and resid 650 through 658 Processing helix chain 'L' and resid 682 through 686 Processing helix chain 'L' and resid 687 through 696 removed outlier: 4.361A pdb=" N ARG L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR L 694 " --> pdb=" O PHE L 690 " (cutoff:3.500A) Processing helix chain 'L' and resid 705 through 709 removed outlier: 3.945A pdb=" N LYS L 709 " --> pdb=" O GLU L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 710 through 715 removed outlier: 3.746A pdb=" N SER L 715 " --> pdb=" O HIS L 712 " (cutoff:3.500A) Processing helix chain 'L' and resid 734 through 749 removed outlier: 4.165A pdb=" N THR L 738 " --> pdb=" O HIS L 734 " (cutoff:3.500A) Processing helix chain 'L' and resid 766 through 784 removed outlier: 3.654A pdb=" N GLU L 783 " --> pdb=" O ASN L 779 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS L 784 " --> pdb=" O PHE L 780 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 removed outlier: 3.882A pdb=" N LEU K 74 " --> pdb=" O THR K 70 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE K 75 " --> pdb=" O VAL K 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 70 through 75' Processing helix chain 'K' and resid 118 through 123 removed outlier: 3.820A pdb=" N LYS K 121 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE K 122 " --> pdb=" O GLY K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 Processing helix chain 'K' and resid 517 through 525 Processing helix chain 'K' and resid 582 through 591 Processing helix chain 'K' and resid 607 through 612 Processing helix chain 'K' and resid 620 through 635 removed outlier: 3.538A pdb=" N LYS K 624 " --> pdb=" O LEU K 620 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET K 627 " --> pdb=" O GLU K 623 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET K 633 " --> pdb=" O ALA K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 650 through 659 removed outlier: 3.887A pdb=" N TYR K 654 " --> pdb=" O ASP K 650 " (cutoff:3.500A) Processing helix chain 'K' and resid 682 through 686 Processing helix chain 'K' and resid 687 through 696 removed outlier: 3.695A pdb=" N ARG K 693 " --> pdb=" O ALA K 689 " (cutoff:3.500A) Processing helix chain 'K' and resid 735 through 748 removed outlier: 3.504A pdb=" N GLN K 744 " --> pdb=" O GLU K 740 " (cutoff:3.500A) Processing helix chain 'K' and resid 766 through 786 removed outlier: 3.788A pdb=" N HIS K 772 " --> pdb=" O SER K 768 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU K 783 " --> pdb=" O ASN K 779 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS K 784 " --> pdb=" O PHE K 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.253A pdb=" N LEU J 105 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL J 115 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN J 107 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER J 113 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 129 through 132 removed outlier: 3.745A pdb=" N ARG J 129 " --> pdb=" O SER J 142 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL J 145 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR J 154 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 192 through 195 removed outlier: 7.151A pdb=" N TYR J 202 " --> pdb=" O ARG J 212 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG J 212 " --> pdb=" O TYR J 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 305 through 307 removed outlier: 6.997A pdb=" N ALA J 241 " --> pdb=" O ALA J 254 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY J 225 " --> pdb=" O ALA J 241 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N TRP J 243 " --> pdb=" O TYR J 223 " (cutoff:3.500A) removed outlier: 16.168A pdb=" N TYR J 223 " --> pdb=" O TRP J 243 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY J 225 " --> pdb=" O ALA J 254 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA J 254 " --> pdb=" O GLY J 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 264 through 266 Processing sheet with id=AA6, first strand: chain 'J' and resid 319 through 325 removed outlier: 5.641A pdb=" N ILE J 321 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU J 337 " --> pdb=" O ILE J 321 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET J 323 " --> pdb=" O THR J 335 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL J 343 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER J 344 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU J 361 " --> pdb=" O SER J 344 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU J 346 " --> pdb=" O LYS J 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 384 through 390 Processing sheet with id=AA8, first strand: chain 'J' and resid 425 through 432 removed outlier: 3.705A pdb=" N LYS J 427 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR J 439 " --> pdb=" O LEU J 429 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR J 431 " --> pdb=" O LYS J 437 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS J 437 " --> pdb=" O TYR J 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 478 through 481 removed outlier: 6.368A pdb=" N VAL J 502 " --> pdb=" O ASP J 513 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP J 513 " --> pdb=" O VAL J 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 531 through 534 removed outlier: 3.834A pdb=" N LYS J 597 " --> pdb=" O GLN J 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU J 549 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL J 595 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N CYS J 598 " --> pdb=" O VAL J 565 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS J 673 " --> pdb=" O VAL J 644 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER J 675 " --> pdb=" O VAL J 646 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY J 648 " --> pdb=" O SER J 675 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN J 755 " --> pdb=" O PHE J 722 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE J 724 " --> pdb=" O GLN J 755 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N TYR J 757 " --> pdb=" O ILE J 724 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N HIS J 726 " --> pdb=" O TYR J 757 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'I' and resid 103 through 107 removed outlier: 6.793A pdb=" N VAL I 103 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AB5, first strand: chain 'I' and resid 192 through 195 removed outlier: 7.083A pdb=" N TYR I 202 " --> pdb=" O ARG I 212 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG I 212 " --> pdb=" O TYR I 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AB7, first strand: chain 'I' and resid 222 through 224 removed outlier: 4.806A pdb=" N LEU I 294 " --> pdb=" O MET I 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 263 through 266 Processing sheet with id=AB9, first strand: chain 'I' and resid 319 through 326 removed outlier: 5.602A pdb=" N ILE I 321 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU I 337 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET I 323 " --> pdb=" O THR I 335 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL I 343 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER I 344 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU I 361 " --> pdb=" O SER I 344 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU I 346 " --> pdb=" O LYS I 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 384 through 390 Processing sheet with id=AC2, first strand: chain 'I' and resid 425 through 432 removed outlier: 6.640A pdb=" N TYR I 439 " --> pdb=" O LEU I 429 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR I 431 " --> pdb=" O LYS I 437 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS I 437 " --> pdb=" O TYR I 431 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 478 through 481 removed outlier: 6.845A pdb=" N VAL I 502 " --> pdb=" O ASP I 513 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP I 513 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 531 through 533 removed outlier: 3.585A pdb=" N LEU I 549 " --> pdb=" O VAL I 595 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL I 595 " --> pdb=" O LEU I 549 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS I 598 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR I 560 " --> pdb=" O ASP I 640 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR I 642 " --> pdb=" O TYR I 560 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU I 562 " --> pdb=" O THR I 642 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL I 644 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU I 564 " --> pdb=" O VAL I 644 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL I 646 " --> pdb=" O LEU I 564 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL I 566 " --> pdb=" O VAL I 646 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLY I 648 " --> pdb=" O VAL I 566 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS I 673 " --> pdb=" O VAL I 644 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY I 648 " --> pdb=" O SER I 675 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE I 722 " --> pdb=" O SER I 753 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLN I 755 " --> pdb=" O PHE I 722 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE I 724 " --> pdb=" O GLN I 755 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TYR I 757 " --> pdb=" O ILE I 724 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N HIS I 726 " --> pdb=" O TYR I 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 537 through 539 Processing sheet with id=AC6, first strand: chain 'L' and resid 103 through 107 removed outlier: 6.731A pdb=" N VAL L 103 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 129 through 132 removed outlier: 3.740A pdb=" N ARG L 129 " --> pdb=" O SER L 142 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL L 145 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR L 154 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 192 through 195 removed outlier: 7.155A pdb=" N TYR L 202 " --> pdb=" O ARG L 212 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG L 212 " --> pdb=" O TYR L 202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 305 through 307 removed outlier: 6.984A pdb=" N ALA L 241 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY L 225 " --> pdb=" O ALA L 241 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N TRP L 243 " --> pdb=" O TYR L 223 " (cutoff:3.500A) removed outlier: 16.174A pdb=" N TYR L 223 " --> pdb=" O TRP L 243 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY L 225 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA L 254 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 264 through 266 Processing sheet with id=AD2, first strand: chain 'L' and resid 319 through 325 removed outlier: 5.634A pdb=" N ILE L 321 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU L 337 " --> pdb=" O ILE L 321 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET L 323 " --> pdb=" O THR L 335 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL L 343 " --> pdb=" O ASN L 338 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER L 344 " --> pdb=" O GLU L 361 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU L 361 " --> pdb=" O SER L 344 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU L 346 " --> pdb=" O LYS L 359 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 384 through 390 Processing sheet with id=AD4, first strand: chain 'L' and resid 425 through 432 removed outlier: 3.675A pdb=" N LYS L 427 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR L 439 " --> pdb=" O LEU L 429 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR L 431 " --> pdb=" O LYS L 437 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS L 437 " --> pdb=" O TYR L 431 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 478 through 481 removed outlier: 6.363A pdb=" N VAL L 502 " --> pdb=" O ASP L 513 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP L 513 " --> pdb=" O VAL L 502 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 531 through 534 removed outlier: 3.508A pdb=" N LYS L 597 " --> pdb=" O GLN L 547 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU L 549 " --> pdb=" O VAL L 595 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL L 595 " --> pdb=" O LEU L 549 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N CYS L 598 " --> pdb=" O VAL L 565 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS L 673 " --> pdb=" O VAL L 644 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER L 675 " --> pdb=" O VAL L 646 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY L 648 " --> pdb=" O SER L 675 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY L 674 " --> pdb=" O LEU L 723 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE L 725 " --> pdb=" O GLY L 674 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA L 676 " --> pdb=" O ILE L 725 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLN L 755 " --> pdb=" O PHE L 722 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE L 724 " --> pdb=" O GLN L 755 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N TYR L 757 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N HIS L 726 " --> pdb=" O TYR L 757 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 537 through 539 Processing sheet with id=AD8, first strand: chain 'K' and resid 103 through 107 removed outlier: 7.009A pdb=" N VAL K 103 " --> pdb=" O LEU K 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AE1, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.974A pdb=" N ILE K 200 " --> pdb=" O VAL K 213 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 213 " --> pdb=" O ILE K 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AE3, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AE4, first strand: chain 'K' and resid 263 through 266 Processing sheet with id=AE5, first strand: chain 'K' and resid 319 through 326 removed outlier: 5.380A pdb=" N ILE K 321 " --> pdb=" O LEU K 337 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU K 337 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET K 323 " --> pdb=" O THR K 335 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL K 343 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU K 348 " --> pdb=" O LYS K 358 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS K 358 " --> pdb=" O LEU K 348 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP K 350 " --> pdb=" O CYS K 356 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS K 356 " --> pdb=" O ASP K 350 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 384 through 390 Processing sheet with id=AE7, first strand: chain 'K' and resid 425 through 432 removed outlier: 5.180A pdb=" N ILE K 428 " --> pdb=" O LEU K 441 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU K 441 " --> pdb=" O ILE K 428 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS K 437 " --> pdb=" O ASP K 432 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 478 through 481 removed outlier: 6.539A pdb=" N VAL K 502 " --> pdb=" O ASP K 513 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP K 513 " --> pdb=" O VAL K 502 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N ASN K 504 " --> pdb=" O MET K 511 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N MET K 511 " --> pdb=" O ASN K 504 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 531 through 533 removed outlier: 3.557A pdb=" N LEU K 549 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL K 595 " --> pdb=" O LEU K 549 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS K 598 " --> pdb=" O VAL K 565 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N TYR K 560 " --> pdb=" O ARG K 643 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ALA K 645 " --> pdb=" O TYR K 560 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU K 562 " --> pdb=" O ALA K 645 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE K 647 " --> pdb=" O LEU K 562 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU K 564 " --> pdb=" O PHE K 647 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS K 673 " --> pdb=" O VAL K 644 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY K 648 " --> pdb=" O SER K 675 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE K 722 " --> pdb=" O SER K 753 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN K 755 " --> pdb=" O PHE K 722 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE K 724 " --> pdb=" O GLN K 755 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR K 757 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS K 726 " --> pdb=" O TYR K 757 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 537 through 539 694 hydrogen bonds defined for protein. 1812 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: 5.05 Time building geometry restraints manager: 2.49 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: 7628 1.34 - 1.46: 4973 1.46 - 1.58: 11375 1.58 - 1.70: 0 1.70 - 1.81: 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 1.365 -0.031 2.34e-02 1.83e+03 1.80e+00 bond pdb=" C ILE K 162 " pdb=" N PRO K 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.79e+00 bond pdb=" N CYS K 468 " pdb=" CA CYS K 468 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" C ILE J 162 " pdb=" N PRO J 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.73e+00 bond pdb=" C ILE L 162 " pdb=" N PRO L 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.73e+00 ... (remaining 24123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 32052 1.77 - 3.54: 601 3.54 - 5.32: 55 5.32 - 7.09: 13 7.09 - 8.86: 3 Bond angle restraints: 32724 Sorted by residual: angle pdb=" C GLN I 626 " pdb=" N MET I 627 " pdb=" CA MET I 627 " ideal model delta sigma weight residual 120.28 115.47 4.81 1.34e+00 5.57e-01 1.29e+01 angle pdb=" N MET J 485 " pdb=" CA MET J 485 " pdb=" CB MET J 485 " ideal model delta sigma weight residual 113.65 109.09 4.56 1.47e+00 4.63e-01 9.60e+00 angle pdb=" C VAL I 586 " pdb=" N MET I 587 " pdb=" CA MET I 587 " ideal model delta sigma weight residual 121.66 116.23 5.43 1.76e+00 3.23e-01 9.51e+00 angle pdb=" N VAL J 714 " pdb=" CA VAL J 714 " pdb=" C VAL J 714 " ideal model delta sigma weight residual 111.88 108.98 2.90 1.06e+00 8.90e-01 7.47e+00 angle pdb=" N VAL L 714 " pdb=" CA VAL L 714 " pdb=" C VAL L 714 " ideal model delta sigma weight residual 111.88 108.99 2.89 1.06e+00 8.90e-01 7.45e+00 ... (remaining 32719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 13047 17.56 - 35.12: 1147 35.12 - 52.68: 182 52.68 - 70.25: 48 70.25 - 87.81: 20 Dihedral angle restraints: 14444 sinusoidal: 5888 harmonic: 8556 Sorted by residual: dihedral pdb=" CB CYS K 474 " pdb=" SG CYS K 474 " pdb=" SG CYS K 492 " pdb=" CB CYS K 492 " ideal model delta sinusoidal sigma weight residual -86.00 -12.82 -73.18 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CB CYS L 465 " pdb=" SG CYS L 465 " pdb=" SG CYS L 468 " pdb=" CB CYS L 468 " ideal model delta sinusoidal sigma weight residual -86.00 -157.60 71.60 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS J 465 " pdb=" SG CYS J 465 " pdb=" SG CYS J 468 " pdb=" CB CYS J 468 " ideal model delta sinusoidal sigma weight residual -86.00 -157.39 71.39 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 14441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2510 0.039 - 0.078: 704 0.078 - 0.118: 282 0.118 - 0.157: 37 0.157 - 0.196: 3 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CB ILE I 659 " pdb=" CA ILE I 659 " pdb=" CG1 ILE I 659 " pdb=" CG2 ILE I 659 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.60e-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 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CB ILE I 162 " pdb=" CA ILE I 162 " pdb=" CG1 ILE I 162 " pdb=" CG2 ILE I 162 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 3533 not shown) Planarity restraints: 4216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 497 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO J 498 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO J 498 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 498 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 497 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO L 498 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 498 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 498 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 83 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO L 84 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " 0.023 5.00e-02 4.00e+02 ... (remaining 4213 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 638 2.68 - 3.23: 23919 3.23 - 3.79: 38895 3.79 - 4.34: 52842 4.34 - 4.90: 83855 Nonbonded interactions: 200149 Sorted by model distance: nonbonded pdb=" O VAL K 69 " pdb=" OG SER K 590 " model vdw 2.124 3.040 nonbonded pdb=" O GLY L 696 " pdb=" OH TYR L 705 " model vdw 2.181 3.040 nonbonded pdb=" O GLY J 696 " pdb=" OH TYR J 705 " model vdw 2.182 3.040 nonbonded pdb=" OD1 ASN J 289 " pdb=" OG SER J 688 " model vdw 2.188 3.040 nonbonded pdb=" OG SER L 160 " pdb=" O GLY L 165 " model vdw 2.197 3.040 ... (remaining 200144 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: 0.01 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 20.770 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 0.035 24144 Z= 0.135 Angle : 0.594 8.862 32756 Z= 0.329 Chirality : 0.043 0.196 3536 Planarity : 0.004 0.044 4216 Dihedral : 13.527 87.808 8908 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.18 % Favored : 91.75 % Rotamer: Outliers : 0.08 % Allowed : 0.42 % Favored : 99.50 % 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: -1.30 (0.15), residues: 2908 helix: -0.31 (0.25), residues: 416 sheet: 0.12 (0.19), residues: 750 loop : -1.51 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 212 TYR 0.018 0.001 TYR K 763 PHE 0.016 0.001 PHE J 722 TRP 0.018 0.001 TRP L 229 HIS 0.007 0.001 HIS I 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (24128) covalent geometry : angle 0.59212 / 0.33 (32724) SS BOND : bond 0.00211 / 0.14 ( 16) SS BOND : angle 1.52342 / 1.00 ( 32) hydrogen bonds : bond 0.21164 / 13.41 ( 690) hydrogen bonds : angle 8.87552 / 5.90 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 707 MET cc_start: 0.6681 (pmm) cc_final: 0.6089 (pmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0869 time to fit residues: 5.7291 Evaluate side-chains 28 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 371 GLN I 779 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.054996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.041097 restraints weight = 46873.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.042372 restraints weight = 30612.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.043181 restraints weight = 23123.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.043682 restraints weight = 19339.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.043965 restraints weight = 17265.001| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24144 Z= 0.146 Angle : 0.633 9.410 32756 Z= 0.352 Chirality : 0.045 0.215 3536 Planarity : 0.004 0.050 4216 Dihedral : 4.627 23.858 3208 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.57 % Favored : 92.02 % Rotamer: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.84 % 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: -1.49 (0.15), residues: 2908 helix: -0.67 (0.24), residues: 492 sheet: 0.02 (0.18), residues: 860 loop : -1.71 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 747 TYR 0.016 0.001 TYR K 274 PHE 0.011 0.001 PHE L 764 TRP 0.012 0.001 TRP J 229 HIS 0.006 0.001 HIS J 772 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (24128) covalent geometry : angle 0.63113 / 0.35 (32724) SS BOND : bond 0.00224 / 0.13 ( 16) SS BOND : angle 1.85914 / 1.29 ( 32) hydrogen bonds : bond 0.05958 / 3.75 ( 690) hydrogen bonds : angle 7.48116 / 4.85 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 97 ARG cc_start: 0.6414 (mmt180) cc_final: 0.5713 (mtp85) REVERT: I 149 TYR cc_start: 0.7629 (m-80) cc_final: 0.7361 (m-80) REVERT: I 763 TYR cc_start: 0.8025 (m-80) cc_final: 0.7755 (m-80) REVERT: I 783 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7680 (mm-30) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.0762 time to fit residues: 4.3095 Evaluate side-chains 28 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 84 optimal weight: 9.9990 chunk 183 optimal weight: 0.0000 chunk 130 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 chunk 94 optimal weight: 0.3980 chunk 202 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 49 optimal weight: 0.0370 overall best weight: 1.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 736 GLN I 737 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.055663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.041785 restraints weight = 46034.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.043173 restraints weight = 28991.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.044062 restraints weight = 21546.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.044607 restraints weight = 17870.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.044812 restraints weight = 15873.248| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24144 Z= 0.121 Angle : 0.588 9.259 32756 Z= 0.325 Chirality : 0.044 0.148 3536 Planarity : 0.003 0.035 4216 Dihedral : 4.317 23.211 3208 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.74 % Favored : 93.12 % Rotamer: Outliers : 0.15 % Allowed : 4.47 % Favored : 95.38 % 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: -1.51 (0.15), residues: 2908 helix: -0.75 (0.23), residues: 492 sheet: 0.01 (0.18), residues: 860 loop : -1.71 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 775 TYR 0.012 0.001 TYR L 654 PHE 0.014 0.001 PHE I 764 TRP 0.009 0.001 TRP J 229 HIS 0.003 0.001 HIS J 772 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (24128) covalent geometry : angle 0.58770 / 0.32 (32724) SS BOND : bond 0.00268 / 0.16 ( 16) SS BOND : angle 0.75387 / 0.50 ( 32) hydrogen bonds : bond 0.05029 / 3.21 ( 690) hydrogen bonds : angle 7.11029 / 4.62 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 763 TYR cc_start: 0.7899 (m-80) cc_final: 0.7624 (m-80) REVERT: I 783 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7697 (mm-30) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.0705 time to fit residues: 4.5905 Evaluate side-chains 30 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 14 optimal weight: 0.0010 chunk 121 optimal weight: 0.9980 chunk 37 optimal weight: 0.0470 chunk 190 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 250 optimal weight: 0.0010 chunk 277 optimal weight: 0.0030 chunk 50 optimal weight: 0.6980 chunk 278 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 overall best weight: 0.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.056981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.042988 restraints weight = 44597.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.044380 restraints weight = 28668.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.045259 restraints weight = 21515.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.045759 restraints weight = 17857.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.046112 restraints weight = 15939.336| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.6882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24144 Z= 0.118 Angle : 0.605 8.588 32756 Z= 0.329 Chirality : 0.044 0.183 3536 Planarity : 0.003 0.032 4216 Dihedral : 4.184 24.002 3208 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.29 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -1.49 (0.15), residues: 2908 helix: -0.66 (0.23), residues: 492 sheet: 0.01 (0.18), residues: 860 loop : -1.71 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 775 TYR 0.014 0.001 TYR L 763 PHE 0.015 0.001 PHE I 764 TRP 0.007 0.001 TRP J 229 HIS 0.003 0.000 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (24128) covalent geometry : angle 0.60442 / 0.33 (32724) SS BOND : bond 0.00670 / 0.40 ( 16) SS BOND : angle 0.97098 / 0.68 ( 32) hydrogen bonds : bond 0.04536 / 2.93 ( 690) hydrogen bonds : angle 6.83876 / 4.45 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 763 TYR cc_start: 0.7939 (m-80) cc_final: 0.7739 (m-80) REVERT: I 783 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7711 (mm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0741 time to fit residues: 4.3469 Evaluate side-chains 33 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 102 optimal weight: 0.3980 chunk 41 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 180 optimal weight: 0.0870 chunk 83 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 32 optimal weight: 0.0050 chunk 213 optimal weight: 0.0970 chunk 266 optimal weight: 0.6980 overall best weight: 0.1368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.057699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.043782 restraints weight = 45437.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.045204 restraints weight = 28729.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.046111 restraints weight = 21404.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.046466 restraints weight = 17727.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.046947 restraints weight = 16026.451| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24144 Z= 0.113 Angle : 0.596 8.325 32756 Z= 0.323 Chirality : 0.044 0.158 3536 Planarity : 0.003 0.031 4216 Dihedral : 4.004 22.114 3208 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.98 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -1.44 (0.15), residues: 2908 helix: -0.61 (0.23), residues: 492 sheet: 0.08 (0.18), residues: 848 loop : -1.70 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 631 TYR 0.017 0.001 TYR K 476 PHE 0.014 0.001 PHE K 764 TRP 0.006 0.001 TRP K 229 HIS 0.002 0.000 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (24128) covalent geometry : angle 0.59545 / 0.32 (32724) SS BOND : bond 0.00244 / 0.14 ( 16) SS BOND : angle 0.94959 / 0.66 ( 32) hydrogen bonds : bond 0.04226 / 2.75 ( 690) hydrogen bonds : angle 6.75839 / 4.40 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 499 MET cc_start: 0.6975 (mmp) cc_final: 0.6183 (mmm) REVERT: I 783 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7708 (mm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0777 time to fit residues: 4.4814 Evaluate side-chains 32 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 39 optimal weight: 0.0050 chunk 227 optimal weight: 0.1980 chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 240 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 285 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 223 optimal weight: 0.0070 chunk 80 optimal weight: 0.0770 chunk 249 optimal weight: 0.0000 overall best weight: 0.0574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.058310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.044678 restraints weight = 45616.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046114 restraints weight = 29127.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.047001 restraints weight = 21700.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.047440 restraints weight = 18033.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047856 restraints weight = 16207.423| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24144 Z= 0.113 Angle : 0.576 8.050 32756 Z= 0.312 Chirality : 0.043 0.144 3536 Planarity : 0.003 0.031 4216 Dihedral : 3.887 21.429 3208 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.70 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -1.37 (0.15), residues: 2908 helix: -0.44 (0.24), residues: 492 sheet: 0.11 (0.18), residues: 840 loop : -1.67 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 617 TYR 0.016 0.001 TYR J 763 PHE 0.013 0.001 PHE J 764 TRP 0.005 0.001 TRP J 336 HIS 0.002 0.000 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (24128) covalent geometry : angle 0.57575 / 0.31 (32724) SS BOND : bond 0.00226 / 0.13 ( 16) SS BOND : angle 0.70882 / 0.49 ( 32) hydrogen bonds : bond 0.03938 / 2.58 ( 690) hydrogen bonds : angle 6.62848 / 4.32 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: I 264 MET cc_start: 0.7531 (mmp) cc_final: 0.7090 (mmp) REVERT: I 499 MET cc_start: 0.7363 (mmp) cc_final: 0.6655 (mmm) REVERT: I 701 ASP cc_start: 0.8193 (t0) cc_final: 0.7867 (t70) REVERT: I 783 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7704 (mm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0698 time to fit residues: 4.3307 Evaluate side-chains 32 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 39 optimal weight: 50.0000 chunk 235 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 130 optimal weight: 0.0170 chunk 173 optimal weight: 0.0170 chunk 40 optimal weight: 0.0020 chunk 81 optimal weight: 0.0020 chunk 22 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 overall best weight: 0.1472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.058566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.044888 restraints weight = 44893.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.046294 restraints weight = 28796.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.047169 restraints weight = 21518.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.047736 restraints weight = 17781.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.048039 restraints weight = 15735.125| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24144 Z= 0.110 Angle : 0.584 9.452 32756 Z= 0.311 Chirality : 0.043 0.139 3536 Planarity : 0.003 0.031 4216 Dihedral : 3.878 25.962 3208 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -1.31 (0.15), residues: 2908 helix: -0.35 (0.24), residues: 492 sheet: 0.18 (0.18), residues: 796 loop : -1.63 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 450 TYR 0.018 0.001 TYR J 763 PHE 0.011 0.001 PHE J 764 TRP 0.010 0.001 TRP L 336 HIS 0.003 0.001 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (24128) covalent geometry : angle 0.58300 / 0.31 (32724) SS BOND : bond 0.00241 / 0.14 ( 16) SS BOND : angle 1.09825 / 0.79 ( 32) hydrogen bonds : bond 0.03738 / 2.46 ( 690) hydrogen bonds : angle 6.52514 / 4.25 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 149 TYR cc_start: 0.7682 (m-80) cc_final: 0.7198 (m-80) REVERT: I 499 MET cc_start: 0.7361 (mmp) cc_final: 0.6651 (mmm) REVERT: I 701 ASP cc_start: 0.8077 (t0) cc_final: 0.7735 (t70) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0612 time to fit residues: 3.8016 Evaluate side-chains 34 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 193 optimal weight: 5.9990 chunk 96 optimal weight: 0.0000 chunk 187 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 22 optimal weight: 0.0040 chunk 248 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 171 optimal weight: 0.0020 chunk 234 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 overall best weight: 1.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.057811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.044140 restraints weight = 44389.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.045513 restraints weight = 28806.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.046392 restraints weight = 21495.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.046930 restraints weight = 17800.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.047292 restraints weight = 15786.091| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.7226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24144 Z= 0.109 Angle : 0.599 8.180 32756 Z= 0.319 Chirality : 0.043 0.143 3536 Planarity : 0.003 0.033 4216 Dihedral : 3.880 26.357 3208 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.12 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -1.24 (0.15), residues: 2908 helix: -0.32 (0.24), residues: 492 sheet: 0.15 (0.18), residues: 840 loop : -1.57 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 97 TYR 0.013 0.001 TYR I 763 PHE 0.010 0.001 PHE L 764 TRP 0.007 0.001 TRP J 336 HIS 0.003 0.000 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (24128) covalent geometry : angle 0.59836 / 0.32 (32724) SS BOND : bond 0.00201 / 0.12 ( 16) SS BOND : angle 1.10784 / 0.79 ( 32) hydrogen bonds : bond 0.03694 / 2.42 ( 690) hydrogen bonds : angle 6.62084 / 4.33 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 97 ARG cc_start: 0.6021 (mmt180) cc_final: 0.5381 (mmt180) REVERT: I 149 TYR cc_start: 0.7400 (m-80) cc_final: 0.6985 (m-80) REVERT: I 499 MET cc_start: 0.7320 (mmp) cc_final: 0.6607 (mmm) REVERT: I 701 ASP cc_start: 0.7937 (t0) cc_final: 0.7643 (t70) REVERT: I 783 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7758 (mm-30) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0697 time to fit residues: 3.7631 Evaluate side-chains 31 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 159 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 97 optimal weight: 8.9990 chunk 282 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.057221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.043299 restraints weight = 45154.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.044710 restraints weight = 28806.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045604 restraints weight = 21530.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.046189 restraints weight = 17848.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.046439 restraints weight = 15789.462| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.7215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24144 Z= 0.111 Angle : 0.590 8.481 32756 Z= 0.315 Chirality : 0.043 0.141 3536 Planarity : 0.003 0.033 4216 Dihedral : 3.890 25.876 3208 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.12 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.21 (0.15), residues: 2908 helix: -0.26 (0.25), residues: 492 sheet: 0.18 (0.18), residues: 844 loop : -1.57 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 527 TYR 0.016 0.001 TYR J 651 PHE 0.010 0.001 PHE L 764 TRP 0.006 0.001 TRP J 336 HIS 0.002 0.001 HIS J 591 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (24128) covalent geometry : angle 0.58943 / 0.31 (32724) SS BOND : bond 0.00158 / 0.09 ( 16) SS BOND : angle 1.05894 / 0.76 ( 32) hydrogen bonds : bond 0.03610 / 2.38 ( 690) hydrogen bonds : angle 6.62908 / 4.33 ( 1812) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: I 97 ARG cc_start: 0.6193 (mmt180) cc_final: 0.5429 (mmt180) REVERT: I 149 TYR cc_start: 0.7485 (m-80) cc_final: 0.6829 (m-80) REVERT: I 499 MET cc_start: 0.7300 (mmp) cc_final: 0.6579 (mmm) REVERT: I 651 TYR cc_start: 0.8224 (t80) cc_final: 0.8018 (t80) REVERT: I 701 ASP cc_start: 0.7949 (t0) cc_final: 0.7666 (t70) REVERT: I 783 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7801 (mm-30) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0664 time to fit residues: 3.6568 Evaluate side-chains 28 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 0.0470 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 0.0470 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 0.4980 chunk 170 optimal weight: 0.4980 chunk 157 optimal weight: 0.0770 chunk 255 optimal weight: 1.9990 chunk 172 optimal weight: 0.0570 chunk 268 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.1452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.058055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.044328 restraints weight = 44463.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.045721 restraints weight = 28842.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.046611 restraints weight = 21537.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.047175 restraints weight = 17800.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.047526 restraints weight = 15759.971| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.7328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24144 Z= 0.109 Angle : 0.594 10.654 32756 Z= 0.315 Chirality : 0.043 0.147 3536 Planarity : 0.003 0.033 4216 Dihedral : 3.888 25.221 3208 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.98 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -1.23 (0.15), residues: 2908 helix: -0.37 (0.24), residues: 492 sheet: 0.19 (0.18), residues: 816 loop : -1.54 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 527 TYR 0.015 0.001 TYR K 651 PHE 0.012 0.001 PHE J 764 TRP 0.006 0.001 TRP J 336 HIS 0.003 0.001 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (24128) covalent geometry : angle 0.59365 / 0.31 (32724) SS BOND : bond 0.00207 / 0.12 ( 16) SS BOND : angle 1.15038 / 0.80 ( 32) hydrogen bonds : bond 0.03659 / 2.42 ( 690) hydrogen bonds : angle 6.60046 / 4.31 ( 1812) ********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 149 TYR cc_start: 0.7319 (m-80) cc_final: 0.6746 (m-80) REVERT: I 323 MET cc_start: 0.5837 (tmm) cc_final: 0.5382 (ptm) REVERT: I 499 MET cc_start: 0.7102 (mmp) cc_final: 0.6366 (mmm) REVERT: I 651 TYR cc_start: 0.8097 (t80) cc_final: 0.7891 (t80) REVERT: I 783 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0565 time to fit residues: 3.2650 Evaluate side-chains 30 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 111 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 0.0570 chunk 28 optimal weight: 4.9990 chunk 158 optimal weight: 0.0770 chunk 133 optimal weight: 0.0030 chunk 20 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 184 optimal weight: 0.0270 chunk 150 optimal weight: 6.9990 overall best weight: 0.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.058586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.045200 restraints weight = 43246.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.046553 restraints weight = 27989.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.047423 restraints weight = 20844.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.048024 restraints weight = 17154.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.048257 restraints weight = 15090.980| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24144 Z= 0.108 Angle : 0.597 11.469 32756 Z= 0.316 Chirality : 0.043 0.207 3536 Planarity : 0.003 0.033 4216 Dihedral : 3.846 25.651 3208 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.57 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.14 (0.15), residues: 2908 helix: -0.08 (0.25), residues: 464 sheet: 0.27 (0.19), residues: 776 loop : -1.51 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 703 TYR 0.015 0.001 TYR L 651 PHE 0.012 0.001 PHE L 764 TRP 0.006 0.001 TRP L 336 HIS 0.003 0.001 HIS K 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (24128) covalent geometry : angle 0.59643 / 0.32 (32724) SS BOND : bond 0.00216 / 0.12 ( 16) SS BOND : angle 1.06462 / 0.75 ( 32) hydrogen bonds : bond 0.03581 / 2.38 ( 690) hydrogen bonds : angle 6.54714 / 4.29 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.56 seconds wall clock time: 32 minutes 59.94 seconds (1979.94 seconds total)