Starting phenix.real_space_refine on Sun Sep 29 21:02:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/09_2024/7e8g_31018.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/09_2024/7e8g_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/09_2024/7e8g_31018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/09_2024/7e8g_31018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/09_2024/7e8g_31018.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/09_2024/7e8g_31018.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.35, per 1000 atoms: 0.57 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: 5.39 Conformation dependent library (CDL) restraints added in 2.9 seconds 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5488 Finding SS restraints... Secondary structure from input PDB file: 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: 3.53 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: 9.69 Time building geometry restraints manager: 6.36 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: 0.00 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: 1.280 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: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 52.490 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 24128 Z= 0.173 Angle : 0.592 8.862 32724 Z= 0.328 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 : 16.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP L 229 HIS 0.007 0.001 HIS I 151 PHE 0.016 0.001 PHE J 722 TYR 0.018 0.001 TYR K 763 ARG 0.004 0.000 ARG K 212 *********************** 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 fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.665 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: 0.2114 time to fit residues: 14.0746 Evaluate side-chains 28 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.4980 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 147 optimal weight: 0.3980 chunk 116 optimal weight: 0.6980 chunk 225 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 261 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 779 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24128 Z= 0.173 Angle : 0.630 9.447 32724 Z= 0.349 Chirality : 0.045 0.240 3536 Planarity : 0.004 0.054 4216 Dihedral : 4.583 23.766 3208 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.74 % Favored : 92.85 % Rotamer: Outliers : 0.15 % Allowed : 3.70 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 2908 helix: -0.68 (0.24), residues: 492 sheet: 0.13 (0.18), residues: 860 loop : -1.70 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 229 HIS 0.006 0.001 HIS L 772 PHE 0.015 0.001 PHE K 764 TYR 0.014 0.001 TYR J 763 ARG 0.005 0.000 ARG L 775 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 145 VAL cc_start: 0.8084 (p) cc_final: 0.7871 (t) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1971 time to fit residues: 12.3722 Evaluate side-chains 30 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 233 optimal weight: 0.0470 chunk 259 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24128 Z= 0.147 Angle : 0.570 9.025 32724 Z= 0.315 Chirality : 0.044 0.154 3536 Planarity : 0.003 0.030 4216 Dihedral : 4.155 21.697 3208 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.70 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 2908 helix: -0.83 (0.23), residues: 496 sheet: -0.02 (0.18), residues: 852 loop : -1.62 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 229 HIS 0.003 0.001 HIS J 772 PHE 0.014 0.001 PHE K 764 TYR 0.015 0.001 TYR J 763 ARG 0.002 0.000 ARG L 775 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 783 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7620 (mm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1914 time to fit residues: 11.0516 Evaluate side-chains 31 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 10.0000 chunk 196 optimal weight: 0.0970 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 278 optimal weight: 10.0000 chunk 137 optimal weight: 0.2980 chunk 249 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.6851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24128 Z= 0.147 Angle : 0.577 8.632 32724 Z= 0.316 Chirality : 0.043 0.184 3536 Planarity : 0.003 0.030 4216 Dihedral : 4.038 20.219 3208 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.84 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 2908 helix: -0.76 (0.23), residues: 492 sheet: -0.04 (0.18), residues: 848 loop : -1.64 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 336 HIS 0.002 0.001 HIS L 772 PHE 0.012 0.001 PHE K 764 TYR 0.018 0.001 TYR K 763 ARG 0.002 0.000 ARG K 775 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 499 MET cc_start: 0.6293 (mmm) cc_final: 0.5956 (mmm) REVERT: I 783 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7614 (mm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1940 time to fit residues: 10.4180 Evaluate side-chains 30 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.0030 chunk 158 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 2.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 737 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24128 Z= 0.156 Angle : 0.577 8.331 32724 Z= 0.315 Chirality : 0.043 0.156 3536 Planarity : 0.003 0.030 4216 Dihedral : 3.994 19.059 3208 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.80 % Favored : 91.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2908 helix: -0.75 (0.23), residues: 492 sheet: -0.13 (0.18), residues: 844 loop : -1.67 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 243 HIS 0.002 0.001 HIS I 591 PHE 0.011 0.001 PHE K 764 TYR 0.012 0.001 TYR K 763 ARG 0.002 0.000 ARG I 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 783 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7652 (mm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2004 time to fit residues: 11.5928 Evaluate side-chains 30 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.9990 chunk 250 optimal weight: 0.0050 chunk 55 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 278 optimal weight: 10.0000 chunk 231 optimal weight: 0.0010 chunk 129 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24128 Z= 0.140 Angle : 0.571 8.335 32724 Z= 0.311 Chirality : 0.043 0.146 3536 Planarity : 0.003 0.030 4216 Dihedral : 3.939 19.968 3208 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.12 % Favored : 91.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 2908 helix: -0.76 (0.23), residues: 492 sheet: -0.11 (0.18), residues: 836 loop : -1.68 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 229 HIS 0.002 0.000 HIS K 281 PHE 0.036 0.001 PHE I 785 TYR 0.014 0.001 TYR J 763 ARG 0.002 0.000 ARG K 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 783 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7625 (mm-30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2024 time to fit residues: 11.3312 Evaluate side-chains 31 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 158 optimal weight: 0.1980 chunk 203 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 277 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 169 optimal weight: 0.0070 chunk 128 optimal weight: 2.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.7109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24128 Z= 0.138 Angle : 0.566 8.961 32724 Z= 0.303 Chirality : 0.043 0.148 3536 Planarity : 0.003 0.029 4216 Dihedral : 3.859 21.719 3208 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 2908 helix: -0.61 (0.24), residues: 492 sheet: -0.15 (0.18), residues: 836 loop : -1.68 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 336 HIS 0.002 0.000 HIS K 281 PHE 0.012 0.001 PHE J 764 TYR 0.015 0.001 TYR L 651 ARG 0.002 0.000 ARG K 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 701 ASP cc_start: 0.7843 (t0) cc_final: 0.7612 (t70) REVERT: I 783 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7594 (mm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2354 time to fit residues: 12.8487 Evaluate side-chains 30 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.0670 chunk 110 optimal weight: 0.0670 chunk 165 optimal weight: 0.0470 chunk 83 optimal weight: 0.0470 chunk 54 optimal weight: 0.0470 chunk 53 optimal weight: 0.0170 chunk 176 optimal weight: 0.0870 chunk 189 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 218 optimal weight: 5.9990 overall best weight: 0.0450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24128 Z= 0.148 Angle : 0.587 8.396 32724 Z= 0.312 Chirality : 0.043 0.143 3536 Planarity : 0.003 0.028 4216 Dihedral : 3.801 18.549 3208 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 2908 helix: -0.63 (0.23), residues: 492 sheet: -0.09 (0.18), residues: 788 loop : -1.68 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 336 HIS 0.002 0.000 HIS I 281 PHE 0.012 0.001 PHE L 764 TYR 0.014 0.001 TYR J 763 ARG 0.002 0.000 ARG J 775 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 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 fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 701 ASP cc_start: 0.7803 (t0) cc_final: 0.7579 (t70) REVERT: I 783 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7563 (mm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1629 time to fit residues: 10.1627 Evaluate side-chains 30 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.0970 chunk 265 optimal weight: 7.9990 chunk 242 optimal weight: 0.0170 chunk 258 optimal weight: 8.9990 chunk 155 optimal weight: 0.0170 chunk 112 optimal weight: 0.0170 chunk 203 optimal weight: 0.0370 chunk 79 optimal weight: 6.9990 chunk 233 optimal weight: 0.4980 chunk 244 optimal weight: 0.4980 chunk 257 optimal weight: 0.8980 overall best weight: 0.0370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24128 Z= 0.142 Angle : 0.580 8.341 32724 Z= 0.307 Chirality : 0.043 0.133 3536 Planarity : 0.003 0.029 4216 Dihedral : 3.743 20.433 3208 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 2908 helix: -0.60 (0.24), residues: 492 sheet: -0.11 (0.19), residues: 764 loop : -1.66 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 336 HIS 0.002 0.001 HIS K 281 PHE 0.012 0.001 PHE J 764 TYR 0.009 0.001 TYR K 763 ARG 0.002 0.000 ARG I 775 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 323 MET cc_start: 0.5477 (tmm) cc_final: 0.5178 (ptp) REVERT: I 783 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7582 (mm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1638 time to fit residues: 9.4367 Evaluate side-chains 28 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9990 chunk 273 optimal weight: 10.0000 chunk 166 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 264 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 23 optimal weight: 0.0370 chunk 176 optimal weight: 0.0060 chunk 140 optimal weight: 2.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24128 Z= 0.143 Angle : 0.585 11.301 32724 Z= 0.308 Chirality : 0.043 0.136 3536 Planarity : 0.003 0.029 4216 Dihedral : 3.753 19.661 3208 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2908 helix: -0.55 (0.24), residues: 488 sheet: -0.10 (0.19), residues: 772 loop : -1.64 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 336 HIS 0.002 0.001 HIS I 281 PHE 0.011 0.001 PHE J 764 TYR 0.025 0.001 TYR L 130 ARG 0.004 0.000 ARG I 703 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 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 fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 323 MET cc_start: 0.5610 (tmm) cc_final: 0.5245 (ptm) REVERT: I 633 MET cc_start: 0.8319 (tpp) cc_final: 0.8047 (mmt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1528 time to fit residues: 8.8437 Evaluate side-chains 29 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 1.9990 chunk 243 optimal weight: 0.0170 chunk 69 optimal weight: 0.4980 chunk 210 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 228 optimal weight: 8.9990 chunk 95 optimal weight: 0.0270 chunk 234 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 overall best weight: 1.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.058533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.044403 restraints weight = 43526.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.045736 restraints weight = 28886.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.046604 restraints weight = 21977.036| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24128 Z= 0.147 Angle : 0.581 8.966 32724 Z= 0.311 Chirality : 0.043 0.140 3536 Planarity : 0.003 0.029 4216 Dihedral : 3.746 20.336 3208 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.15), residues: 2908 helix: -0.74 (0.24), residues: 492 sheet: -0.25 (0.18), residues: 828 loop : -1.61 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 336 HIS 0.002 0.000 HIS K 281 PHE 0.010 0.001 PHE J 764 TYR 0.008 0.001 TYR I 763 ARG 0.003 0.000 ARG J 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2758.80 seconds wall clock time: 51 minutes 39.81 seconds (3099.81 seconds total)