Starting phenix.real_space_refine on Thu Feb 5 04:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oaj_70287/02_2026/9oaj_70287.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oaj_70287/02_2026/9oaj_70287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oaj_70287/02_2026/9oaj_70287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oaj_70287/02_2026/9oaj_70287.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oaj_70287/02_2026/9oaj_70287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oaj_70287/02_2026/9oaj_70287.map" } resolution = 2.91 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= 0.057 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 102 5.16 5 C 9204 2.51 5 N 2499 2.21 5 O 2868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14673 Number of models: 1 Model: "" Number of chains: 21 Chain: "C" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "B" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1133 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 1, 'TRANS': 139} Chain breaks: 1 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2818 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 18, 'TRANS': 339} Chain breaks: 4 Chain: "D" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1133 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 1, 'TRANS': 139} Chain breaks: 1 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2818 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 18, 'TRANS': 339} Chain breaks: 4 Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "H" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1133 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 1, 'TRANS': 139} Chain breaks: 1 Chain: "I" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2818 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 18, 'TRANS': 339} Chain breaks: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.25, per 1000 atoms: 0.22 Number of scatterers: 14673 At special positions: 0 Unit cell: (129.642, 135.966, 105.4, 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 102 16.00 O 2868 8.00 N 2499 7.00 C 9204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS A 501 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.01 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.09 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.14 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 605 " - pdb=" SG CYS F 501 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.05 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.06 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.12 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.07 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 109 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 605 " - pdb=" SG CYS I 501 " distance=2.02 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.02 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.05 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.07 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.07 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 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 241 " " NAG A 603 " - " ASN A 289 " " NAG A 604 " - " ASN A 362 " " NAG A 605 " - " ASN A 386 " " NAG A 606 " - " ASN A 295 " " NAG B 701 " - " ASN B 625 " " NAG E 701 " - " ASN E 625 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 241 " " NAG F 603 " - " ASN F 289 " " NAG F 604 " - " ASN F 362 " " NAG F 605 " - " ASN F 386 " " NAG F 606 " - " ASN F 295 " " NAG H 701 " - " ASN H 625 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 241 " " NAG I 603 " - " ASN I 289 " " NAG I 604 " - " ASN I 362 " " NAG I 605 " - " ASN I 386 " " NAG I 606 " - " ASN I 295 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 276 " " NAG L 1 " - " ASN F 262 " " NAG M 1 " - " ASN F 276 " " NAG N 1 " - " ASN I 262 " " NAG O 1 " - " ASN I 276 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 606.4 milliseconds 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3366 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 27 sheets defined 33.0% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'C' and resid 83 through 90 removed outlier: 4.221A pdb=" N ASP C 88 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.351A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.854A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 561 through 563 No H-bonds generated for 'chain 'B' and resid 561 through 563' Processing helix chain 'B' and resid 564 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.619A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.150A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 removed outlier: 4.018A pdb=" N ASN A 392 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.587A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 90 removed outlier: 4.330A pdb=" N ASP D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.236A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.832A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 546 through 551 removed outlier: 3.929A pdb=" N GLN E 550 " --> pdb=" O SER E 546 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN E 551 " --> pdb=" O GLY E 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 546 through 551' Processing helix chain 'E' and resid 561 through 563 No H-bonds generated for 'chain 'E' and resid 561 through 563' Processing helix chain 'E' and resid 564 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.542A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.185A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.507A pdb=" N CYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 396 through 405 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.608A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 90 removed outlier: 4.302A pdb=" N ASP G 88 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 104 Processing helix chain 'H' and resid 523 through 528 removed outlier: 4.303A pdb=" N GLY H 527 " --> pdb=" O GLY H 524 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 534 Processing helix chain 'H' and resid 536 through 542 removed outlier: 3.794A pdb=" N GLN H 540 " --> pdb=" O THR H 536 " (cutoff:3.500A) Processing helix chain 'H' and resid 543 through 545 No H-bonds generated for 'chain 'H' and resid 543 through 545' Processing helix chain 'H' and resid 548 through 552 Processing helix chain 'H' and resid 561 through 563 No H-bonds generated for 'chain 'H' and resid 561 through 563' Processing helix chain 'H' and resid 564 through 596 Processing helix chain 'H' and resid 618 through 626 removed outlier: 3.538A pdb=" N MET H 626 " --> pdb=" O ILE H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 635 Processing helix chain 'H' and resid 638 through 662 Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.146A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 127 removed outlier: 3.527A pdb=" N CYS I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 353 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.052A pdb=" N ASN I 392 " --> pdb=" O LYS I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 405 Processing helix chain 'I' and resid 475 through 484 removed outlier: 3.586A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 32 removed outlier: 3.693A pdb=" N LYS C 27 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE C 51 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY C 63 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 53 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AA3, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.008A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.789A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.974A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.516A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.172A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 334 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.879A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 32 removed outlier: 3.611A pdb=" N LYS D 27 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE D 51 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 63 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP D 53 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AB3, first strand: chain 'E' and resid 603 through 609 removed outlier: 8.095A pdb=" N CYS E 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR F 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR E 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL F 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL E 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.799A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.929A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'F' and resid 200 through 203 removed outlier: 5.596A pdb=" N VAL F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR F 435 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 259 through 261 removed outlier: 9.766A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N SER F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N VAL F 292 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER F 334 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.976A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N VAL F 292 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N SER F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE F 467 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE F 468 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 32 removed outlier: 3.806A pdb=" N LYS G 27 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE G 51 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY G 63 " --> pdb=" O PHE G 51 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP G 53 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 37 through 39 Processing sheet with id=AC3, first strand: chain 'H' and resid 603 through 609 removed outlier: 8.021A pdb=" N CYS H 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N TYR I 40 " --> pdb=" O CYS H 604 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR H 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL I 38 " --> pdb=" O THR H 606 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL H 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.817A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 75 through 76 removed outlier: 6.921A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'I' and resid 200 through 203 removed outlier: 5.628A pdb=" N VAL I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR I 435 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 259 through 261 removed outlier: 9.958A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N SER I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N VAL I 292 " --> pdb=" O SER I 446 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER I 334 " --> pdb=" O VAL I 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.037A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N VAL I 292 " --> pdb=" O SER I 446 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N SER I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE I 467 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE I 468 " --> pdb=" O THR I 358 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3252 1.33 - 1.45: 3335 1.45 - 1.58: 8206 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 14931 Sorted by residual: bond pdb=" CG GLN H 540 " pdb=" CD GLN H 540 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.28e+00 bond pdb=" CG GLN B 540 " pdb=" CD GLN B 540 " ideal model delta sigma weight residual 1.516 1.441 0.075 2.50e-02 1.60e+03 8.98e+00 bond pdb=" NE ARG C 84 " pdb=" CZ ARG C 84 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.37e+00 bond pdb=" NE ARG D 84 " pdb=" CZ ARG D 84 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.10e-02 8.26e+03 6.61e+00 bond pdb=" NE ARG G 84 " pdb=" CZ ARG G 84 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.10e-02 8.26e+03 6.49e+00 ... (remaining 14926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 17845 1.65 - 3.31: 2015 3.31 - 4.96: 261 4.96 - 6.62: 87 6.62 - 8.27: 18 Bond angle restraints: 20226 Sorted by residual: angle pdb=" C ALA I 436 " pdb=" N PRO I 437 " pdb=" CA PRO I 437 " ideal model delta sigma weight residual 119.66 125.61 -5.95 7.20e-01 1.93e+00 6.83e+01 angle pdb=" C ALA F 436 " pdb=" N PRO F 437 " pdb=" CA PRO F 437 " ideal model delta sigma weight residual 119.66 125.35 -5.69 7.20e-01 1.93e+00 6.24e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 125.20 -5.54 7.20e-01 1.93e+00 5.92e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.15 -7.59 1.01e+00 9.80e-01 5.64e+01 angle pdb=" C GLU I 492 " pdb=" N PRO I 493 " pdb=" CA PRO I 493 " ideal model delta sigma weight residual 119.56 126.95 -7.39 1.01e+00 9.80e-01 5.35e+01 ... (remaining 20221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 9115 18.05 - 36.10: 261 36.10 - 54.15: 75 54.15 - 72.20: 31 72.20 - 90.26: 13 Dihedral angle restraints: 9495 sinusoidal: 4332 harmonic: 5163 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -176.26 90.26 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -174.75 88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -173.69 87.69 1 1.00e+01 1.00e-02 9.21e+01 ... (remaining 9492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1845 0.079 - 0.157: 489 0.157 - 0.236: 50 0.236 - 0.314: 5 0.314 - 0.393: 5 Chirality restraints: 2394 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.61e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.61e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.60e+01 ... (remaining 2391 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 295 " -0.055 2.00e-02 2.50e+03 5.61e-02 3.94e+01 pdb=" CG ASN A 295 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 295 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 295 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A 606 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 295 " 0.049 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" CG ASN I 295 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN I 295 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN I 295 " -0.079 2.00e-02 2.50e+03 pdb=" C1 NAG I 606 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 625 " 0.048 2.00e-02 2.50e+03 4.94e-02 3.05e+01 pdb=" CG ASN E 625 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN E 625 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN E 625 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG E 701 " 0.060 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 7079 2.97 - 3.45: 12951 3.45 - 3.94: 24847 3.94 - 4.42: 27169 4.42 - 4.90: 45187 Nonbonded interactions: 117233 Sorted by model distance: nonbonded pdb=" NZ LYS F 231 " pdb=" OE1 GLU F 267 " model vdw 2.491 3.120 nonbonded pdb=" OG1 THR A 336 " pdb=" O GLY A 410 " model vdw 2.496 3.040 nonbonded pdb=" O CYS F 126 " pdb=" C VAL F 127 " model vdw 2.497 3.270 nonbonded pdb=" O CYS I 126 " pdb=" C VAL I 127 " model vdw 2.498 3.270 nonbonded pdb=" O CYS A 126 " pdb=" C VAL A 127 " model vdw 2.499 3.270 ... (remaining 117228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.012 0.110 14997 Z= 0.640 Angle : 1.208 11.884 20391 Z= 0.788 Chirality : 0.069 0.393 2394 Planarity : 0.005 0.020 2538 Dihedral : 10.581 89.667 6030 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 1743 helix: 0.12 (0.21), residues: 429 sheet: 1.57 (0.23), residues: 402 loop : 2.24 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.019 0.003 TYR I 40 PHE 0.018 0.004 PHE A 383 TRP 0.029 0.005 TRP I 479 HIS 0.003 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.01149 (14931) covalent geometry : angle 1.15029 (20226) SS BOND : bond 0.03107 ( 33) SS BOND : angle 3.84916 ( 66) hydrogen bonds : bond 0.18895 ( 607) hydrogen bonds : angle 7.25073 ( 1632) link_BETA1-4 : bond 0.04815 ( 6) link_BETA1-4 : angle 6.02334 ( 18) link_NAG-ASN : bond 0.07583 ( 27) link_NAG-ASN : angle 4.13422 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 589 ASP cc_start: 0.7750 (m-30) cc_final: 0.7336 (m-30) REVERT: B 662 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 393 SER cc_start: 0.7659 (p) cc_final: 0.7334 (m) REVERT: F 348 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7860 (mmtp) REVERT: H 637 ASN cc_start: 0.7832 (m-40) cc_final: 0.7615 (m-40) REVERT: I 490 ARG cc_start: 0.8345 (ttp-110) cc_final: 0.8127 (ttm110) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.5800 time to fit residues: 173.1835 Evaluate side-chains 173 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 52 HIS C 65 GLN B 637 ASN A 103 GLN A 114 GLN A 216 GLN A 249 HIS D 52 HIS D 65 GLN D 77 ASN E 575 GLN E 577 GLN E 624 ASN F 82 GLN F 103 GLN F 249 HIS ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN H 624 ASN I 103 GLN I 105 HIS I 114 GLN I 216 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.199058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150075 restraints weight = 13970.906| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.28 r_work: 0.3359 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14997 Z= 0.143 Angle : 0.584 10.353 20391 Z= 0.302 Chirality : 0.046 0.220 2394 Planarity : 0.004 0.056 2538 Dihedral : 4.693 30.066 2562 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.37 % Allowed : 7.51 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.20), residues: 1743 helix: 1.48 (0.24), residues: 444 sheet: 1.56 (0.24), residues: 414 loop : 1.55 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 490 TYR 0.014 0.001 TYR I 384 PHE 0.017 0.002 PHE F 383 TRP 0.019 0.001 TRP I 479 HIS 0.006 0.002 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00320 (14931) covalent geometry : angle 0.56379 (20226) SS BOND : bond 0.00341 ( 33) SS BOND : angle 0.84486 ( 66) hydrogen bonds : bond 0.05547 ( 607) hydrogen bonds : angle 5.28571 ( 1632) link_BETA1-4 : bond 0.00410 ( 6) link_BETA1-4 : angle 1.69723 ( 18) link_NAG-ASN : bond 0.00470 ( 27) link_NAG-ASN : angle 2.32556 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: B 518 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6735 (mtm) REVERT: B 585 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7793 (mtm-85) REVERT: B 589 ASP cc_start: 0.8312 (m-30) cc_final: 0.8083 (m-30) REVERT: B 662 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 393 SER cc_start: 0.8064 (p) cc_final: 0.7729 (m) REVERT: A 394 THR cc_start: 0.7390 (t) cc_final: 0.7161 (m) REVERT: A 425 ASN cc_start: 0.8064 (m110) cc_final: 0.7856 (m110) REVERT: E 577 GLN cc_start: 0.8833 (mt0) cc_final: 0.8630 (mt0) REVERT: F 348 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7302 (mmtp) REVERT: F 393 SER cc_start: 0.8224 (p) cc_final: 0.7898 (m) REVERT: F 504 ARG cc_start: 0.6807 (mtt180) cc_final: 0.6550 (mtt180) REVERT: H 637 ASN cc_start: 0.8178 (m-40) cc_final: 0.7907 (m-40) REVERT: I 87 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: I 267 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7742 (mp0) REVERT: I 373 MET cc_start: 0.6889 (mtp) cc_final: 0.6559 (mmt) REVERT: I 382 PHE cc_start: 0.7960 (m-80) cc_final: 0.7742 (m-80) REVERT: I 399 ASP cc_start: 0.6894 (m-30) cc_final: 0.6218 (t0) REVERT: I 492 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8466 (mm-30) outliers start: 22 outliers final: 4 residues processed: 202 average time/residue: 0.6190 time to fit residues: 135.8189 Evaluate side-chains 165 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 601 LYS Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 164 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 133 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 330 HIS E 575 GLN E 652 GLN F 105 HIS G 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.192338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144231 restraints weight = 14115.213| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.47 r_work: 0.3282 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14997 Z= 0.180 Angle : 0.588 10.834 20391 Z= 0.300 Chirality : 0.047 0.178 2394 Planarity : 0.004 0.052 2538 Dihedral : 4.929 38.827 2562 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.17 % Allowed : 8.69 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.80 (0.20), residues: 1743 helix: 1.66 (0.24), residues: 444 sheet: 1.42 (0.23), residues: 447 loop : 0.99 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 490 TYR 0.016 0.002 TYR I 384 PHE 0.014 0.002 PHE I 53 TRP 0.023 0.002 TRP A 479 HIS 0.004 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00433 (14931) covalent geometry : angle 0.56629 (20226) SS BOND : bond 0.00432 ( 33) SS BOND : angle 1.01161 ( 66) hydrogen bonds : bond 0.05443 ( 607) hydrogen bonds : angle 5.17906 ( 1632) link_BETA1-4 : bond 0.00485 ( 6) link_BETA1-4 : angle 1.38141 ( 18) link_NAG-ASN : bond 0.00269 ( 27) link_NAG-ASN : angle 2.38444 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: B 518 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6876 (mtp) REVERT: B 589 ASP cc_start: 0.8260 (m-30) cc_final: 0.8022 (m-30) REVERT: B 662 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 350 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7942 (mtp85) REVERT: A 393 SER cc_start: 0.8152 (p) cc_final: 0.7924 (m) REVERT: A 394 THR cc_start: 0.7548 (t) cc_final: 0.7346 (m) REVERT: A 479 TRP cc_start: 0.7069 (m-10) cc_final: 0.6540 (m100) REVERT: D 75 LYS cc_start: 0.7733 (pttm) cc_final: 0.7362 (mmtp) REVERT: E 636 ASP cc_start: 0.7989 (t0) cc_final: 0.7785 (t0) REVERT: E 658 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: F 393 SER cc_start: 0.8205 (p) cc_final: 0.7935 (m) REVERT: F 479 TRP cc_start: 0.6972 (m-10) cc_final: 0.6192 (m100) REVERT: G 75 LYS cc_start: 0.7652 (pttt) cc_final: 0.7380 (mmtp) REVERT: H 589 ASP cc_start: 0.8230 (m-30) cc_final: 0.8023 (m-30) REVERT: H 637 ASN cc_start: 0.8321 (m-40) cc_final: 0.8080 (m-40) REVERT: I 87 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: I 373 MET cc_start: 0.7118 (mtp) cc_final: 0.6676 (mmt) REVERT: I 393 SER cc_start: 0.8304 (p) cc_final: 0.7996 (m) REVERT: I 399 ASP cc_start: 0.6987 (m-30) cc_final: 0.6364 (t0) outliers start: 35 outliers final: 13 residues processed: 196 average time/residue: 0.6878 time to fit residues: 145.4873 Evaluate side-chains 176 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 601 LYS Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 649 SER Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 375 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 160 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 HIS C 58 GLN A 82 GLN A 114 GLN A 330 HIS E 577 GLN E 652 GLN G 65 GLN I 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.191214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.143420 restraints weight = 14069.728| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.41 r_work: 0.3275 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14997 Z= 0.160 Angle : 0.537 9.118 20391 Z= 0.275 Chirality : 0.045 0.169 2394 Planarity : 0.004 0.042 2538 Dihedral : 4.944 45.942 2562 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.48 % Allowed : 9.56 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.20), residues: 1743 helix: 1.76 (0.25), residues: 444 sheet: 1.27 (0.23), residues: 447 loop : 0.68 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 350 TYR 0.013 0.001 TYR F 384 PHE 0.013 0.002 PHE D 51 TRP 0.014 0.001 TRP F 479 HIS 0.005 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00386 (14931) covalent geometry : angle 0.52004 (20226) SS BOND : bond 0.00323 ( 33) SS BOND : angle 1.20574 ( 66) hydrogen bonds : bond 0.04882 ( 607) hydrogen bonds : angle 5.03844 ( 1632) link_BETA1-4 : bond 0.00449 ( 6) link_BETA1-4 : angle 1.20433 ( 18) link_NAG-ASN : bond 0.00226 ( 27) link_NAG-ASN : angle 1.92034 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6814 (mtp) REVERT: A 348 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7309 (mmtp) REVERT: A 393 SER cc_start: 0.8228 (p) cc_final: 0.7906 (m) REVERT: A 394 THR cc_start: 0.7849 (t) cc_final: 0.7585 (m) REVERT: A 429 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6801 (mp0) REVERT: A 479 TRP cc_start: 0.7196 (m-10) cc_final: 0.6646 (m100) REVERT: A 504 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6618 (mtt180) REVERT: E 567 GLN cc_start: 0.7140 (tp40) cc_final: 0.6896 (tt0) REVERT: E 577 GLN cc_start: 0.8916 (mt0) cc_final: 0.8703 (mt0) REVERT: E 658 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: F 479 TRP cc_start: 0.7115 (m-10) cc_final: 0.6268 (m100) REVERT: G 75 LYS cc_start: 0.7676 (pttt) cc_final: 0.7370 (mmtp) REVERT: H 629 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8583 (mmm) REVERT: H 637 ASN cc_start: 0.8386 (m-40) cc_final: 0.8157 (m-40) REVERT: H 658 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: I 87 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: I 231 LYS cc_start: 0.7824 (mttm) cc_final: 0.7274 (mttp) REVERT: I 283 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8028 (m) REVERT: I 393 SER cc_start: 0.8518 (p) cc_final: 0.8166 (m) REVERT: I 399 ASP cc_start: 0.7026 (m-30) cc_final: 0.6368 (t0) REVERT: I 447 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7957 (m) outliers start: 40 outliers final: 11 residues processed: 188 average time/residue: 0.7272 time to fit residues: 147.2380 Evaluate side-chains 170 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 601 LYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain H residue 518 MET Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain H residue 649 SER Chi-restraints excluded: chain H residue 658 GLN Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 447 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 158 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 330 HIS D 52 HIS E 575 GLN E 652 GLN H 554 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.190440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142582 restraints weight = 14119.955| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.42 r_work: 0.3269 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14997 Z= 0.159 Angle : 0.529 8.830 20391 Z= 0.271 Chirality : 0.045 0.177 2394 Planarity : 0.004 0.039 2538 Dihedral : 5.040 48.263 2562 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.55 % Allowed : 9.75 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1743 helix: 1.78 (0.25), residues: 444 sheet: 1.22 (0.23), residues: 447 loop : 0.50 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 350 TYR 0.011 0.001 TYR A 384 PHE 0.013 0.002 PHE D 51 TRP 0.013 0.001 TRP I 479 HIS 0.006 0.001 HIS G 52 Details of bonding type rmsd covalent geometry : bond 0.00382 (14931) covalent geometry : angle 0.51419 (20226) SS BOND : bond 0.00313 ( 33) SS BOND : angle 1.02093 ( 66) hydrogen bonds : bond 0.04799 ( 607) hydrogen bonds : angle 5.03552 ( 1632) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 1.13206 ( 18) link_NAG-ASN : bond 0.00197 ( 27) link_NAG-ASN : angle 1.78768 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6371 (mtt) REVERT: B 520 LEU cc_start: 0.7905 (tp) cc_final: 0.7554 (mp) REVERT: A 215 ILE cc_start: 0.8346 (mt) cc_final: 0.7930 (tt) REVERT: A 348 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7241 (mmtp) REVERT: A 393 SER cc_start: 0.8142 (p) cc_final: 0.7796 (m) REVERT: A 429 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6737 (mp0) REVERT: A 479 TRP cc_start: 0.7085 (m-10) cc_final: 0.6598 (m100) REVERT: A 504 ARG cc_start: 0.6988 (mtt180) cc_final: 0.6632 (mtt180) REVERT: E 518 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.5826 (mmt) REVERT: E 658 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: F 479 TRP cc_start: 0.6945 (m-10) cc_final: 0.6104 (m100) REVERT: G 75 LYS cc_start: 0.7683 (pttt) cc_final: 0.7398 (mmtp) REVERT: G 81 ASP cc_start: 0.7524 (t0) cc_final: 0.7166 (t0) REVERT: H 574 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8045 (mtpm) REVERT: H 629 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8572 (mmm) REVERT: H 637 ASN cc_start: 0.8485 (m-40) cc_final: 0.8253 (m-40) REVERT: H 658 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: I 231 LYS cc_start: 0.7872 (mttm) cc_final: 0.7338 (mttp) REVERT: I 399 ASP cc_start: 0.7090 (m-30) cc_final: 0.6462 (t0) REVERT: I 447 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.8106 (m) outliers start: 41 outliers final: 14 residues processed: 187 average time/residue: 0.7356 time to fit residues: 148.5779 Evaluate side-chains 171 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 601 LYS Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain H residue 518 MET Chi-restraints excluded: chain H residue 574 LYS Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain H residue 649 SER Chi-restraints excluded: chain H residue 658 GLN Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 137 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 425 ASN E 652 GLN F 114 GLN F 448 ASN I 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.190196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142405 restraints weight = 14022.784| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.43 r_work: 0.3256 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14997 Z= 0.156 Angle : 0.530 8.711 20391 Z= 0.271 Chirality : 0.045 0.175 2394 Planarity : 0.004 0.039 2538 Dihedral : 5.127 49.281 2562 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.48 % Allowed : 9.87 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1743 helix: 1.78 (0.25), residues: 444 sheet: 1.16 (0.24), residues: 447 loop : 0.41 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 490 TYR 0.010 0.001 TYR I 384 PHE 0.014 0.002 PHE A 383 TRP 0.013 0.001 TRP I 479 HIS 0.005 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00375 (14931) covalent geometry : angle 0.51517 (20226) SS BOND : bond 0.00355 ( 33) SS BOND : angle 1.21773 ( 66) hydrogen bonds : bond 0.04698 ( 607) hydrogen bonds : angle 5.05413 ( 1632) link_BETA1-4 : bond 0.00437 ( 6) link_BETA1-4 : angle 1.10009 ( 18) link_NAG-ASN : bond 0.00187 ( 27) link_NAG-ASN : angle 1.71753 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6481 (mtt) REVERT: B 574 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7787 (mtpm) REVERT: A 215 ILE cc_start: 0.8397 (mt) cc_final: 0.8035 (tt) REVERT: A 348 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7285 (mmtp) REVERT: A 389 LYS cc_start: 0.7625 (mptt) cc_final: 0.7116 (mtmt) REVERT: A 393 SER cc_start: 0.8230 (p) cc_final: 0.7885 (m) REVERT: A 479 TRP cc_start: 0.7106 (m-10) cc_final: 0.6613 (m100) REVERT: E 518 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.5867 (mmt) REVERT: E 658 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: F 479 TRP cc_start: 0.6990 (m-10) cc_final: 0.6342 (m100) REVERT: G 75 LYS cc_start: 0.7702 (pttt) cc_final: 0.7380 (mmtp) REVERT: G 81 ASP cc_start: 0.7656 (t0) cc_final: 0.7223 (t0) REVERT: H 574 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8075 (mtpm) REVERT: H 629 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8571 (mmm) REVERT: H 637 ASN cc_start: 0.8614 (m-40) cc_final: 0.8411 (m-40) REVERT: H 658 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: I 399 ASP cc_start: 0.7147 (m-30) cc_final: 0.6549 (t0) REVERT: I 447 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8266 (m) REVERT: I 492 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8407 (mm-30) outliers start: 40 outliers final: 15 residues processed: 181 average time/residue: 0.7482 time to fit residues: 146.3274 Evaluate side-chains 168 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain H residue 518 MET Chi-restraints excluded: chain H residue 574 LYS Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 649 SER Chi-restraints excluded: chain H residue 658 GLN Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 492 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN E 652 GLN F 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.198567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.151371 restraints weight = 13815.774| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.04 r_work: 0.3401 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14997 Z= 0.201 Angle : 0.583 9.298 20391 Z= 0.296 Chirality : 0.046 0.185 2394 Planarity : 0.004 0.040 2538 Dihedral : 5.418 50.497 2562 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.92 % Allowed : 9.93 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1743 helix: 1.39 (0.25), residues: 462 sheet: 1.01 (0.24), residues: 447 loop : 0.26 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 490 TYR 0.012 0.002 TYR F 384 PHE 0.015 0.002 PHE F 383 TRP 0.014 0.001 TRP B 571 HIS 0.005 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00493 (14931) covalent geometry : angle 0.56692 (20226) SS BOND : bond 0.00553 ( 33) SS BOND : angle 1.41753 ( 66) hydrogen bonds : bond 0.05083 ( 607) hydrogen bonds : angle 5.22693 ( 1632) link_BETA1-4 : bond 0.00469 ( 6) link_BETA1-4 : angle 1.07255 ( 18) link_NAG-ASN : bond 0.00213 ( 27) link_NAG-ASN : angle 1.85075 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: B 518 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6353 (mtt) REVERT: B 520 LEU cc_start: 0.8340 (tp) cc_final: 0.7982 (mp) REVERT: B 574 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7946 (mtpm) REVERT: B 585 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.7696 (mtm-85) REVERT: A 215 ILE cc_start: 0.8428 (mt) cc_final: 0.8165 (tt) REVERT: A 348 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7394 (mmtp) REVERT: A 479 TRP cc_start: 0.7193 (m-10) cc_final: 0.6594 (m100) REVERT: D 81 ASP cc_start: 0.7890 (t70) cc_final: 0.7230 (t0) REVERT: E 518 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6672 (mtm) REVERT: E 658 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: F 479 TRP cc_start: 0.7087 (m-10) cc_final: 0.6357 (m100) REVERT: F 490 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7933 (ttp80) REVERT: G 75 LYS cc_start: 0.7639 (pttt) cc_final: 0.7322 (mmtm) REVERT: H 574 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8267 (mtpm) REVERT: H 629 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8651 (mmm) REVERT: H 637 ASN cc_start: 0.8699 (m-40) cc_final: 0.8418 (m-40) REVERT: H 658 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: I 399 ASP cc_start: 0.7304 (m-30) cc_final: 0.6698 (t0) outliers start: 47 outliers final: 20 residues processed: 180 average time/residue: 0.7500 time to fit residues: 146.0384 Evaluate side-chains 165 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain H residue 518 MET Chi-restraints excluded: chain H residue 574 LYS Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 649 SER Chi-restraints excluded: chain H residue 658 GLN Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 339 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 104 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 173 optimal weight: 0.0970 chunk 157 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.0050 chunk 98 optimal weight: 0.5980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 GLN E 577 GLN E 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.201755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154331 restraints weight = 13871.606| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.08 r_work: 0.3453 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14997 Z= 0.116 Angle : 0.489 8.811 20391 Z= 0.254 Chirality : 0.043 0.155 2394 Planarity : 0.004 0.039 2538 Dihedral : 5.223 50.788 2562 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.05 % Allowed : 11.17 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1743 helix: 1.68 (0.25), residues: 462 sheet: 1.11 (0.24), residues: 447 loop : 0.34 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.009 0.001 TYR F 384 PHE 0.012 0.001 PHE C 51 TRP 0.015 0.001 TRP I 479 HIS 0.005 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00267 (14931) covalent geometry : angle 0.47279 (20226) SS BOND : bond 0.00456 ( 33) SS BOND : angle 1.30326 ( 66) hydrogen bonds : bond 0.04177 ( 607) hydrogen bonds : angle 4.99460 ( 1632) link_BETA1-4 : bond 0.00348 ( 6) link_BETA1-4 : angle 1.08272 ( 18) link_NAG-ASN : bond 0.00138 ( 27) link_NAG-ASN : angle 1.63342 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6405 (mtt) REVERT: B 520 LEU cc_start: 0.8391 (tp) cc_final: 0.8081 (OUTLIER) REVERT: B 574 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7752 (mtpm) REVERT: B 585 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.7667 (mtm-85) REVERT: A 82 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: A 215 ILE cc_start: 0.8442 (mt) cc_final: 0.8221 (tt) REVERT: A 479 TRP cc_start: 0.6968 (m-10) cc_final: 0.6595 (m100) REVERT: E 518 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6660 (mtm) REVERT: E 658 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: F 399 ASP cc_start: 0.6927 (m-30) cc_final: 0.6237 (t0) REVERT: F 479 TRP cc_start: 0.6939 (m-10) cc_final: 0.6197 (m100) REVERT: G 75 LYS cc_start: 0.7655 (pttt) cc_final: 0.7313 (mmtm) REVERT: H 520 LEU cc_start: 0.8385 (tp) cc_final: 0.8012 (mp) REVERT: H 574 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8194 (mtpm) REVERT: H 585 ARG cc_start: 0.8373 (mtp-110) cc_final: 0.7616 (mtm110) REVERT: H 637 ASN cc_start: 0.8729 (m-40) cc_final: 0.8453 (m-40) REVERT: H 658 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: I 399 ASP cc_start: 0.7235 (m-30) cc_final: 0.6670 (t0) REVERT: I 448 ASN cc_start: 0.8558 (m-40) cc_final: 0.8256 (t0) REVERT: I 492 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8376 (mm-30) outliers start: 33 outliers final: 16 residues processed: 175 average time/residue: 0.7679 time to fit residues: 144.7385 Evaluate side-chains 165 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain H residue 574 LYS Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 649 SER Chi-restraints excluded: chain H residue 658 GLN Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 492 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 170 optimal weight: 0.0170 chunk 127 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN E 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.200175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152413 restraints weight = 13829.272| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.07 r_work: 0.3434 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14997 Z= 0.154 Angle : 0.525 8.192 20391 Z= 0.269 Chirality : 0.044 0.162 2394 Planarity : 0.004 0.038 2538 Dihedral : 5.275 54.748 2562 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.05 % Allowed : 11.61 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1743 helix: 1.54 (0.25), residues: 465 sheet: 0.99 (0.25), residues: 420 loop : 0.23 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 350 TYR 0.009 0.001 TYR I 384 PHE 0.014 0.002 PHE A 53 TRP 0.012 0.001 TRP B 571 HIS 0.005 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00371 (14931) covalent geometry : angle 0.50925 (20226) SS BOND : bond 0.00444 ( 33) SS BOND : angle 1.35190 ( 66) hydrogen bonds : bond 0.04507 ( 607) hydrogen bonds : angle 5.09224 ( 1632) link_BETA1-4 : bond 0.00414 ( 6) link_BETA1-4 : angle 1.02807 ( 18) link_NAG-ASN : bond 0.00162 ( 27) link_NAG-ASN : angle 1.67030 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: B 518 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6420 (mtt) REVERT: B 520 LEU cc_start: 0.8375 (tp) cc_final: 0.8046 (mp) REVERT: B 574 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7821 (mtpm) REVERT: B 585 ARG cc_start: 0.8495 (mtp-110) cc_final: 0.7692 (mtm-85) REVERT: A 82 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: A 389 LYS cc_start: 0.7516 (mptt) cc_final: 0.7077 (mtmt) REVERT: A 479 TRP cc_start: 0.7043 (m-10) cc_final: 0.6530 (m100) REVERT: E 518 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6679 (mtm) REVERT: E 658 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: F 479 TRP cc_start: 0.6980 (m-10) cc_final: 0.6233 (m100) REVERT: G 75 LYS cc_start: 0.7630 (pttt) cc_final: 0.7330 (mmtm) REVERT: H 520 LEU cc_start: 0.8402 (tp) cc_final: 0.7993 (mp) REVERT: H 574 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8219 (mtpm) REVERT: H 637 ASN cc_start: 0.8752 (m-40) cc_final: 0.8458 (m-40) REVERT: H 658 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: I 283 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7933 (m) REVERT: I 399 ASP cc_start: 0.7253 (m-30) cc_final: 0.6686 (t0) REVERT: I 447 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8110 (m) outliers start: 33 outliers final: 17 residues processed: 165 average time/residue: 0.7295 time to fit residues: 129.7989 Evaluate side-chains 163 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain H residue 574 LYS Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 649 SER Chi-restraints excluded: chain H residue 658 GLN Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 652 GLN H 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.200134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152798 restraints weight = 13846.665| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.09 r_work: 0.3435 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14997 Z= 0.153 Angle : 0.535 10.243 20391 Z= 0.275 Chirality : 0.044 0.164 2394 Planarity : 0.004 0.040 2538 Dihedral : 5.336 59.657 2562 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.99 % Allowed : 11.79 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1743 helix: 1.58 (0.25), residues: 462 sheet: 0.94 (0.25), residues: 420 loop : 0.21 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 490 TYR 0.009 0.001 TYR I 384 PHE 0.013 0.002 PHE I 53 TRP 0.012 0.001 TRP B 571 HIS 0.005 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00369 (14931) covalent geometry : angle 0.51958 (20226) SS BOND : bond 0.00474 ( 33) SS BOND : angle 1.43284 ( 66) hydrogen bonds : bond 0.04519 ( 607) hydrogen bonds : angle 5.15838 ( 1632) link_BETA1-4 : bond 0.00456 ( 6) link_BETA1-4 : angle 1.02933 ( 18) link_NAG-ASN : bond 0.00153 ( 27) link_NAG-ASN : angle 1.67693 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: B 518 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6465 (mtt) REVERT: B 574 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7869 (mtpm) REVERT: B 585 ARG cc_start: 0.8484 (mtp-110) cc_final: 0.7680 (mtm-85) REVERT: A 82 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: A 389 LYS cc_start: 0.7567 (mptt) cc_final: 0.7119 (mtmt) REVERT: A 479 TRP cc_start: 0.7038 (m-10) cc_final: 0.6536 (m100) REVERT: D 52 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.5248 (t70) REVERT: E 518 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6671 (mtm) REVERT: E 658 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: F 399 ASP cc_start: 0.6973 (m-30) cc_final: 0.6278 (t0) REVERT: F 479 TRP cc_start: 0.6965 (m-10) cc_final: 0.6187 (m100) REVERT: G 75 LYS cc_start: 0.7599 (pttt) cc_final: 0.7316 (mmtp) REVERT: H 520 LEU cc_start: 0.8396 (tp) cc_final: 0.8011 (mp) REVERT: H 574 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8251 (mtpm) REVERT: H 637 ASN cc_start: 0.8777 (m-40) cc_final: 0.8461 (m-40) REVERT: H 658 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: I 283 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.7938 (m) REVERT: I 399 ASP cc_start: 0.7286 (m-30) cc_final: 0.6731 (t0) outliers start: 32 outliers final: 17 residues processed: 166 average time/residue: 0.7048 time to fit residues: 126.6354 Evaluate side-chains 161 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain H residue 574 LYS Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 649 SER Chi-restraints excluded: chain H residue 658 GLN Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 136 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 HIS E 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.199908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.152720 restraints weight = 13839.730| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.03 r_work: 0.3439 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14997 Z= 0.156 Angle : 0.541 8.959 20391 Z= 0.277 Chirality : 0.044 0.165 2394 Planarity : 0.004 0.042 2538 Dihedral : 5.346 52.259 2562 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.99 % Allowed : 11.98 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1743 helix: 1.57 (0.25), residues: 462 sheet: 0.94 (0.25), residues: 420 loop : 0.20 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 490 TYR 0.009 0.001 TYR I 384 PHE 0.013 0.002 PHE A 53 TRP 0.014 0.001 TRP I 479 HIS 0.005 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00377 (14931) covalent geometry : angle 0.52520 (20226) SS BOND : bond 0.00440 ( 33) SS BOND : angle 1.47614 ( 66) hydrogen bonds : bond 0.04529 ( 607) hydrogen bonds : angle 5.15708 ( 1632) link_BETA1-4 : bond 0.00418 ( 6) link_BETA1-4 : angle 1.02235 ( 18) link_NAG-ASN : bond 0.00148 ( 27) link_NAG-ASN : angle 1.70392 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4281.38 seconds wall clock time: 73 minutes 50.38 seconds (4430.38 seconds total)