Starting phenix.real_space_refine on Wed Mar 4 16:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x5c_22049/03_2026/6x5c_22049.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x5c_22049/03_2026/6x5c_22049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x5c_22049/03_2026/6x5c_22049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x5c_22049/03_2026/6x5c_22049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x5c_22049/03_2026/6x5c_22049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x5c_22049/03_2026/6x5c_22049.map" } resolution = 4.04 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= 0.004 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 93 5.16 5 C 9212 2.51 5 N 2508 2.21 5 O 2831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14644 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2745 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain breaks: 5 Chain: "B" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "D" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2752 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain breaks: 5 Chain: "F" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1156 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "I" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2719 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain breaks: 5 Chain: "G" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1176 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "J" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UOV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UOV': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UOV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.28, per 1000 atoms: 0.22 Number of scatterers: 14644 At special positions: 0 Unit cell: (152.95, 143.75, 109.25, 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 93 16.00 O 2831 8.00 N 2508 7.00 C 9212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.07 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.14 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.06 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.09 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 16 " - pdb=" SG CYS J 84 " distance=2.02 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 ALPHA1-2 " MAN H 4 " - " MAN H 5 " " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG A 601 " - " ASN A 241 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 362 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 413 " " NAG A 613 " - " ASN A 448 " " NAG A 614 " - " ASN A 234 " " NAG D 601 " - " ASN D 241 " " NAG D 607 " - " ASN D 276 " " NAG D 608 " - " ASN D 295 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 362 " " NAG D 611 " - " ASN D 386 " " NAG D 612 " - " ASN D 413 " " NAG D 613 " - " ASN D 448 " " NAG E 608 " - " ASN E 276 " " NAG E 609 " - " ASN E 295 " " NAG E 610 " - " ASN E 332 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG H 1 " - " ASN A 262 " " NAG K 1 " - " ASN D 262 " " NAG L 1 " - " ASN E 241 " " NAG M 1 " - " ASN E 262 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 480.1 milliseconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 28 sheets defined 29.5% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 65 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.659A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.962A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 566 through 593 removed outlier: 3.960A pdb=" N TRP B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.243A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 659 Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.520A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 334 through 353 removed outlier: 4.056A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 483 removed outlier: 3.774A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 524 removed outlier: 3.890A pdb=" N GLY F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 546 Processing helix chain 'F' and resid 561 through 565 Processing helix chain 'F' and resid 566 through 593 removed outlier: 3.969A pdb=" N TRP F 571 " --> pdb=" O GLN F 567 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.665A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.252A pdb=" N LYS F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 659 Processing helix chain 'I' and resid 58 through 64 removed outlier: 4.914A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 79 Processing helix chain 'E' and resid 64 through 72 removed outlier: 3.832A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 114 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 479 through 484 Processing helix chain 'G' and resid 520 through 526 removed outlier: 3.520A pdb=" N GLY G 524 " --> pdb=" O LEU G 520 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 546 Processing helix chain 'G' and resid 561 through 565 Processing helix chain 'G' and resid 567 through 593 Processing helix chain 'G' and resid 594 through 597 Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 removed outlier: 4.129A pdb=" N LYS G 633 " --> pdb=" O MET G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 658 Processing helix chain 'J' and resid 58 through 64 removed outlier: 4.194A pdb=" N ASP J 63 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 500 removed outlier: 5.223A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 199 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.597A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.173A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.779A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.173A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.978A pdb=" N PHE C 26 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY C 38 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP C 28 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB1, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.494A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 202 Processing sheet with id=AB6, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.630A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN D 417 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.742A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.630A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 2 through 5 removed outlier: 3.589A pdb=" N LYS I 2 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE I 26 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASN I 30 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS I 35 " --> pdb=" O ASN I 30 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 14 through 17 Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.267A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'E' and resid 199 through 202 Processing sheet with id=AC7, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.622A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.622A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN E 417 " --> pdb=" O ASN E 386 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 2 through 5 removed outlier: 6.609A pdb=" N LYS J 2 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU J 96 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL J 4 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE J 26 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY J 38 " --> pdb=" O PHE J 26 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP J 28 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY J 38 " --> pdb=" O THR J 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 12 through 17 608 hydrogen bonds defined for protein. 1578 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: 2.24 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2719 1.32 - 1.45: 4574 1.45 - 1.59: 7424 1.59 - 1.73: 83 1.73 - 1.86: 124 Bond restraints: 14924 Sorted by residual: bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.68e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.56e+01 bond pdb=" CB HIS E 66 " pdb=" CG HIS E 66 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.40e+01 bond pdb=" CB ASP J 63 " pdb=" CG ASP J 63 " ideal model delta sigma weight residual 1.516 1.676 -0.160 2.50e-02 1.60e+03 4.10e+01 bond pdb=" NE ARG D 504 " pdb=" CZ ARG D 504 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.07e+01 ... (remaining 14919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 17508 2.49 - 4.98: 2369 4.98 - 7.47: 312 7.47 - 9.96: 34 9.96 - 12.45: 9 Bond angle restraints: 20232 Sorted by residual: angle pdb=" N VAL I 12 " pdb=" CA VAL I 12 " pdb=" C VAL I 12 " ideal model delta sigma weight residual 110.82 121.89 -11.07 9.70e-01 1.06e+00 1.30e+02 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.78 128.43 -8.65 1.03e+00 9.43e-01 7.05e+01 angle pdb=" N VAL D 65 " pdb=" CA VAL D 65 " pdb=" C VAL D 65 " ideal model delta sigma weight residual 110.42 117.95 -7.53 9.60e-01 1.09e+00 6.16e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.87 127.82 -7.95 1.04e+00 9.25e-01 5.85e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.03e+00 9.43e-01 5.56e+01 ... (remaining 20227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 9266 21.82 - 43.65: 175 43.65 - 65.47: 94 65.47 - 87.29: 27 87.29 - 109.12: 13 Dihedral angle restraints: 9575 sinusoidal: 4457 harmonic: 5118 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 -166.36 80.36 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.21 77.21 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.05 77.05 1 1.00e+01 1.00e-02 7.45e+01 ... (remaining 9572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1679 0.110 - 0.220: 510 0.220 - 0.329: 119 0.329 - 0.439: 60 0.439 - 0.549: 18 Chirality restraints: 2386 Sorted by residual: 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 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.67e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.66e+01 ... (remaining 2383 not shown) Planarity restraints: 2553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 392 " -0.071 2.00e-02 2.50e+03 7.49e-02 7.01e+01 pdb=" CG ASN E 392 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 392 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 392 " 0.117 2.00e-02 2.50e+03 pdb=" C1 NAG E 612 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.069 2.00e-02 2.50e+03 7.11e-02 6.32e+01 pdb=" CG ASN A 234 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.109 2.00e-02 2.50e+03 pdb=" C1 NAG A 614 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 241 " -0.059 2.00e-02 2.50e+03 6.22e-02 4.84e+01 pdb=" CG ASN A 241 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 241 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 241 " 0.095 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.077 2.00e-02 2.50e+03 ... (remaining 2550 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5829 2.91 - 3.41: 13618 3.41 - 3.90: 24940 3.90 - 4.40: 29064 4.40 - 4.90: 45774 Nonbonded interactions: 119225 Sorted by model distance: nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 121 " model vdw 2.409 3.120 nonbonded pdb=" NZ LYS E 231 " pdb=" OE1 GLU E 267 " model vdw 2.411 3.120 nonbonded pdb=" NZ LYS D 231 " pdb=" OE1 GLU D 267 " model vdw 2.420 3.120 nonbonded pdb=" OD1 ASP D 113 " pdb=" NZ LYS D 121 " model vdw 2.426 3.120 nonbonded pdb=" N ASN A 301 " pdb=" N ASN A 302 " model vdw 2.429 2.560 ... (remaining 119220 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' and (resid 33 through 124 or resid 197 through 305 or resid 325 throu \ gh 353 or resid 362 through 457 or resid 468 through 611)) selection = (chain 'D' and (resid 33 through 124 or resid 197 through 353 or resid 362 throu \ gh 611)) selection = (chain 'E' and (resid 33 through 305 or resid 325 through 457 or resid 468 throu \ gh 613)) } ncs_group { reference = (chain 'B' and (resid 517 through 659 or resid 800)) selection = (chain 'F' and (resid 517 through 659 or resid 800)) selection = (chain 'G' and resid 517 through 800) } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 13.730 Find NCS groups from input model: 0.330 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.022 0.160 14994 Z= 1.134 Angle : 1.778 12.451 20412 Z= 1.154 Chirality : 0.129 0.549 2386 Planarity : 0.009 0.041 2526 Dihedral : 12.108 109.119 6155 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.24 (0.19), residues: 1728 helix: 0.04 (0.24), residues: 423 sheet: 0.61 (0.26), residues: 383 loop : 0.16 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 54 TYR 0.047 0.008 TYR B 638 PHE 0.036 0.007 PHE D 382 TRP 0.077 0.010 TRP E 479 HIS 0.013 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.02120 (14924) covalent geometry : angle 1.75929 (20232) SS BOND : bond 0.02724 ( 30) SS BOND : angle 3.02065 ( 60) hydrogen bonds : bond 0.16493 ( 586) hydrogen bonds : angle 8.06738 ( 1578) link_ALPHA1-2 : bond 0.07996 ( 3) link_ALPHA1-2 : angle 4.39102 ( 9) link_ALPHA1-3 : bond 0.05539 ( 3) link_ALPHA1-3 : angle 2.28801 ( 9) link_BETA1-4 : bond 0.06867 ( 7) link_BETA1-4 : angle 5.42123 ( 21) link_NAG-ASN : bond 0.08586 ( 27) link_NAG-ASN : angle 2.61349 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7301 (mmtt) REVERT: A 434 MET cc_start: 0.6612 (tmm) cc_final: 0.5431 (mtt) REVERT: B 567 GLN cc_start: 0.8014 (tp40) cc_final: 0.7781 (tm-30) REVERT: B 656 ASN cc_start: 0.8820 (m-40) cc_final: 0.8408 (m-40) REVERT: C 34 ILE cc_start: 0.8180 (mm) cc_final: 0.7852 (mm) REVERT: C 83 ILE cc_start: 0.5422 (tp) cc_final: 0.5212 (tp) REVERT: D 35 TRP cc_start: 0.6836 (m100) cc_final: 0.6611 (m100) REVERT: D 62 ASP cc_start: 0.5790 (p0) cc_final: 0.5489 (t0) REVERT: D 104 MET cc_start: 0.8686 (ttt) cc_final: 0.8427 (tpp) REVERT: D 260 LEU cc_start: 0.7283 (mt) cc_final: 0.6935 (tp) REVERT: D 279 ASP cc_start: 0.7906 (p0) cc_final: 0.7349 (t70) REVERT: D 416 LEU cc_start: 0.8742 (mt) cc_final: 0.8442 (mp) REVERT: I 67 PHE cc_start: 0.8356 (m-80) cc_final: 0.8059 (m-80) REVERT: I 70 ILE cc_start: 0.7902 (mt) cc_final: 0.7233 (mm) REVERT: I 73 ASN cc_start: 0.8481 (t0) cc_final: 0.7770 (t0) REVERT: I 89 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7095 (mp10) REVERT: E 40 TYR cc_start: 0.8239 (t80) cc_final: 0.7956 (t80) REVERT: E 96 TRP cc_start: 0.8228 (m-90) cc_final: 0.7996 (m-10) REVERT: E 97 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8506 (mtmt) REVERT: G 548 ILE cc_start: 0.9013 (mt) cc_final: 0.8792 (tp) REVERT: J 13 GLU cc_start: 0.4638 (tt0) cc_final: 0.3785 (pp20) REVERT: J 36 ILE cc_start: 0.8735 (mt) cc_final: 0.8321 (mp) REVERT: J 86 VAL cc_start: 0.7663 (t) cc_final: 0.7357 (p) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.1392 time to fit residues: 87.4955 Evaluate side-chains 202 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 GLN E 474 ASN G 640 GLN J 33 GLN J 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.120895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.106871 restraints weight = 42498.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.109320 restraints weight = 24882.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.110804 restraints weight = 16386.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.112038 restraints weight = 12114.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.112807 restraints weight = 9471.458| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14994 Z= 0.198 Angle : 0.778 9.524 20412 Z= 0.400 Chirality : 0.050 0.218 2386 Planarity : 0.006 0.135 2526 Dihedral : 8.818 75.121 2730 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 0.20 (0.20), residues: 1728 helix: 0.89 (0.26), residues: 423 sheet: 0.28 (0.27), residues: 357 loop : -0.20 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 273 TYR 0.035 0.003 TYR D 484 PHE 0.017 0.002 PHE A 383 TRP 0.028 0.002 TRP I 28 HIS 0.008 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00439 (14924) covalent geometry : angle 0.75331 (20232) SS BOND : bond 0.00811 ( 30) SS BOND : angle 1.22714 ( 60) hydrogen bonds : bond 0.05393 ( 586) hydrogen bonds : angle 6.09748 ( 1578) link_ALPHA1-2 : bond 0.00217 ( 3) link_ALPHA1-2 : angle 2.36945 ( 9) link_ALPHA1-3 : bond 0.01212 ( 3) link_ALPHA1-3 : angle 2.72810 ( 9) link_BETA1-4 : bond 0.00638 ( 7) link_BETA1-4 : angle 3.55383 ( 21) link_NAG-ASN : bond 0.00511 ( 27) link_NAG-ASN : angle 2.18611 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6419 (tm-30) REVERT: A 113 ASP cc_start: 0.8838 (t70) cc_final: 0.8573 (t0) REVERT: A 434 MET cc_start: 0.6232 (tmm) cc_final: 0.5158 (mtt) REVERT: B 629 MET cc_start: 0.7413 (mmm) cc_final: 0.7146 (tpt) REVERT: D 35 TRP cc_start: 0.6061 (m100) cc_final: 0.5825 (m100) REVERT: D 279 ASP cc_start: 0.7315 (p0) cc_final: 0.6716 (t70) REVERT: D 475 MET cc_start: 0.6886 (mmm) cc_final: 0.6540 (mmm) REVERT: F 539 VAL cc_start: 0.8963 (t) cc_final: 0.8629 (p) REVERT: I 67 PHE cc_start: 0.7978 (m-80) cc_final: 0.6974 (m-10) REVERT: I 73 ASN cc_start: 0.8524 (t0) cc_final: 0.8024 (t0) REVERT: E 476 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.7134 (ttm170) REVERT: G 570 VAL cc_start: 0.8583 (m) cc_final: 0.8246 (t) REVERT: G 618 THR cc_start: 0.7650 (p) cc_final: 0.7125 (p) REVERT: J 13 GLU cc_start: 0.5140 (tt0) cc_final: 0.4366 (pp20) REVERT: J 36 ILE cc_start: 0.8531 (mt) cc_final: 0.8228 (mp) REVERT: J 66 ASN cc_start: 0.8591 (t0) cc_final: 0.8318 (t0) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1115 time to fit residues: 50.6960 Evaluate side-chains 171 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 3 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.120134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.105832 restraints weight = 43157.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.108323 restraints weight = 25106.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.109976 restraints weight = 16513.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.111124 restraints weight = 12006.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.111923 restraints weight = 9430.070| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14994 Z= 0.149 Angle : 0.659 8.461 20412 Z= 0.341 Chirality : 0.047 0.207 2386 Planarity : 0.005 0.116 2526 Dihedral : 7.358 58.203 2730 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 0.05 (0.20), residues: 1728 helix: 0.81 (0.26), residues: 440 sheet: 0.20 (0.27), residues: 349 loop : -0.34 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 585 TYR 0.032 0.002 TYR D 484 PHE 0.022 0.002 PHE J 43 TRP 0.031 0.002 TRP E 45 HIS 0.013 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00329 (14924) covalent geometry : angle 0.64390 (20232) SS BOND : bond 0.00275 ( 30) SS BOND : angle 0.98168 ( 60) hydrogen bonds : bond 0.04482 ( 586) hydrogen bonds : angle 5.61312 ( 1578) link_ALPHA1-2 : bond 0.00411 ( 3) link_ALPHA1-2 : angle 2.12054 ( 9) link_ALPHA1-3 : bond 0.01155 ( 3) link_ALPHA1-3 : angle 1.66594 ( 9) link_BETA1-4 : bond 0.00433 ( 7) link_BETA1-4 : angle 2.74041 ( 21) link_NAG-ASN : bond 0.00340 ( 27) link_NAG-ASN : angle 1.53494 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6598 (tm-30) REVERT: A 113 ASP cc_start: 0.8832 (t70) cc_final: 0.8568 (t0) REVERT: A 434 MET cc_start: 0.6236 (tmm) cc_final: 0.5272 (mtt) REVERT: C 20 GLN cc_start: 0.8109 (mp10) cc_final: 0.7909 (mp10) REVERT: D 279 ASP cc_start: 0.7381 (p0) cc_final: 0.6765 (t70) REVERT: D 434 MET cc_start: 0.7074 (ttt) cc_final: 0.6856 (ttt) REVERT: F 539 VAL cc_start: 0.8912 (t) cc_final: 0.8639 (p) REVERT: I 67 PHE cc_start: 0.7921 (m-80) cc_final: 0.7419 (m-80) REVERT: I 73 ASN cc_start: 0.8454 (t0) cc_final: 0.8063 (t0) REVERT: E 203 GLN cc_start: 0.8483 (mt0) cc_final: 0.7855 (mp-120) REVERT: G 570 VAL cc_start: 0.8503 (m) cc_final: 0.8289 (t) REVERT: G 588 ARG cc_start: 0.8055 (ptt-90) cc_final: 0.7271 (ptt90) REVERT: J 13 GLU cc_start: 0.5223 (tt0) cc_final: 0.4701 (pp20) REVERT: J 61 LEU cc_start: 0.8959 (mm) cc_final: 0.8638 (mm) REVERT: J 66 ASN cc_start: 0.8570 (t0) cc_final: 0.8235 (t0) REVERT: J 82 TYR cc_start: 0.5903 (m-80) cc_final: 0.5683 (m-80) REVERT: J 94 GLN cc_start: 0.6412 (tt0) cc_final: 0.5826 (tp-100) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1007 time to fit residues: 39.6929 Evaluate side-chains 174 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 35 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN B 562 GLN C 40 GLN C 52 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN G 591 GLN J 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.115324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.101098 restraints weight = 43709.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.103406 restraints weight = 25672.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.104973 restraints weight = 17311.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.106087 restraints weight = 12798.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.106854 restraints weight = 10169.636| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 14994 Z= 0.213 Angle : 0.730 11.711 20412 Z= 0.374 Chirality : 0.049 0.211 2386 Planarity : 0.005 0.092 2526 Dihedral : 6.653 56.068 2730 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1728 helix: 0.84 (0.26), residues: 436 sheet: 0.12 (0.28), residues: 361 loop : -0.54 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 588 TYR 0.035 0.003 TYR D 484 PHE 0.021 0.002 PHE B 518 TRP 0.034 0.002 TRP E 96 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00481 (14924) covalent geometry : angle 0.70660 (20232) SS BOND : bond 0.00459 ( 30) SS BOND : angle 2.11459 ( 60) hydrogen bonds : bond 0.04450 ( 586) hydrogen bonds : angle 5.43704 ( 1578) link_ALPHA1-2 : bond 0.00621 ( 3) link_ALPHA1-2 : angle 2.25342 ( 9) link_ALPHA1-3 : bond 0.00844 ( 3) link_ALPHA1-3 : angle 2.54065 ( 9) link_BETA1-4 : bond 0.00307 ( 7) link_BETA1-4 : angle 2.77001 ( 21) link_NAG-ASN : bond 0.00259 ( 27) link_NAG-ASN : angle 1.78272 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6632 (tm-30) REVERT: A 113 ASP cc_start: 0.8896 (t70) cc_final: 0.8641 (t0) REVERT: A 434 MET cc_start: 0.6726 (tmm) cc_final: 0.5923 (mtt) REVERT: D 279 ASP cc_start: 0.7703 (p0) cc_final: 0.6998 (t70) REVERT: F 539 VAL cc_start: 0.8950 (t) cc_final: 0.8687 (p) REVERT: I 34 ILE cc_start: 0.7993 (mm) cc_final: 0.7613 (mm) REVERT: I 67 PHE cc_start: 0.7969 (m-80) cc_final: 0.7371 (m-80) REVERT: I 73 ASN cc_start: 0.8537 (t0) cc_final: 0.8222 (t0) REVERT: E 99 ASN cc_start: 0.8493 (p0) cc_final: 0.8251 (p0) REVERT: E 203 GLN cc_start: 0.8664 (mt0) cc_final: 0.8028 (mp-120) REVERT: G 588 ARG cc_start: 0.8151 (ptt-90) cc_final: 0.7344 (ptt90) REVERT: J 13 GLU cc_start: 0.4913 (tt0) cc_final: 0.4527 (pp20) REVERT: J 61 LEU cc_start: 0.8979 (mm) cc_final: 0.8522 (mm) REVERT: J 66 ASN cc_start: 0.8720 (t0) cc_final: 0.8505 (t0) REVERT: J 94 GLN cc_start: 0.6826 (tt0) cc_final: 0.6162 (tp-100) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1066 time to fit residues: 39.8368 Evaluate side-chains 163 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 94 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 43 optimal weight: 0.0040 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 656 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS F 656 ASN G 564 HIS J 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.118518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.104216 restraints weight = 43148.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.106664 restraints weight = 25270.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.108303 restraints weight = 16625.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.109458 restraints weight = 12120.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.110196 restraints weight = 9524.780| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14994 Z= 0.131 Angle : 0.645 10.488 20412 Z= 0.330 Chirality : 0.047 0.242 2386 Planarity : 0.005 0.081 2526 Dihedral : 6.004 52.779 2730 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.06 % Allowed : 1.41 % Favored : 98.53 % 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: -0.18 (0.20), residues: 1728 helix: 0.93 (0.26), residues: 432 sheet: 0.13 (0.28), residues: 353 loop : -0.69 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 579 TYR 0.027 0.002 TYR D 484 PHE 0.012 0.001 PHE B 518 TRP 0.027 0.002 TRP I 28 HIS 0.005 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00290 (14924) covalent geometry : angle 0.62571 (20232) SS BOND : bond 0.00288 ( 30) SS BOND : angle 1.88261 ( 60) hydrogen bonds : bond 0.03948 ( 586) hydrogen bonds : angle 5.26451 ( 1578) link_ALPHA1-2 : bond 0.00445 ( 3) link_ALPHA1-2 : angle 2.17036 ( 9) link_ALPHA1-3 : bond 0.01075 ( 3) link_ALPHA1-3 : angle 1.53757 ( 9) link_BETA1-4 : bond 0.00388 ( 7) link_BETA1-4 : angle 2.15796 ( 21) link_NAG-ASN : bond 0.00236 ( 27) link_NAG-ASN : angle 1.56132 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6530 (tm-30) REVERT: A 113 ASP cc_start: 0.8885 (t70) cc_final: 0.8683 (t0) REVERT: A 264 SER cc_start: 0.8803 (t) cc_final: 0.8510 (m) REVERT: A 434 MET cc_start: 0.6682 (tmm) cc_final: 0.5803 (mtt) REVERT: B 584 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7567 (mt-10) REVERT: D 217 TYR cc_start: 0.7591 (m-80) cc_final: 0.7331 (m-80) REVERT: D 279 ASP cc_start: 0.7491 (p0) cc_final: 0.6684 (t70) REVERT: F 539 VAL cc_start: 0.8956 (t) cc_final: 0.8617 (p) REVERT: F 626 MET cc_start: 0.7856 (ttm) cc_final: 0.7627 (mtp) REVERT: I 36 ILE cc_start: 0.8106 (mm) cc_final: 0.7899 (mm) REVERT: I 67 PHE cc_start: 0.7931 (m-80) cc_final: 0.7343 (m-80) REVERT: I 73 ASN cc_start: 0.8478 (t0) cc_final: 0.8056 (t0) REVERT: E 80 ASN cc_start: 0.7727 (m-40) cc_final: 0.6459 (p0) REVERT: E 99 ASN cc_start: 0.8431 (p0) cc_final: 0.8111 (p0) REVERT: E 203 GLN cc_start: 0.8653 (mt0) cc_final: 0.8078 (mp-120) REVERT: E 377 ASN cc_start: 0.8169 (t0) cc_final: 0.7602 (t0) REVERT: G 588 ARG cc_start: 0.8032 (ptt-90) cc_final: 0.7235 (ptt90) REVERT: J 13 GLU cc_start: 0.4690 (tt0) cc_final: 0.4447 (pp20) REVERT: J 61 LEU cc_start: 0.8714 (mm) cc_final: 0.8433 (mt) REVERT: J 66 ASN cc_start: 0.8416 (t0) cc_final: 0.7977 (t0) REVERT: J 82 TYR cc_start: 0.6200 (m-80) cc_final: 0.5958 (m-80) REVERT: J 94 GLN cc_start: 0.6781 (tt0) cc_final: 0.6260 (tp-100) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.1124 time to fit residues: 41.4783 Evaluate side-chains 166 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 127 optimal weight: 0.2980 chunk 15 optimal weight: 0.0970 chunk 47 optimal weight: 6.9990 overall best weight: 1.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.117453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.103440 restraints weight = 43446.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105856 restraints weight = 25402.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.107497 restraints weight = 16763.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.108491 restraints weight = 12199.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.109363 restraints weight = 9759.855| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14994 Z= 0.143 Angle : 0.631 9.953 20412 Z= 0.325 Chirality : 0.046 0.196 2386 Planarity : 0.004 0.063 2526 Dihedral : 5.697 54.418 2730 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.06 % Allowed : 0.96 % Favored : 98.98 % 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: -0.19 (0.20), residues: 1728 helix: 1.04 (0.27), residues: 431 sheet: 0.17 (0.28), residues: 361 loop : -0.78 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 585 TYR 0.023 0.002 TYR D 486 PHE 0.014 0.001 PHE B 518 TRP 0.039 0.002 TRP D 112 HIS 0.006 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00323 (14924) covalent geometry : angle 0.61358 (20232) SS BOND : bond 0.00378 ( 30) SS BOND : angle 1.75462 ( 60) hydrogen bonds : bond 0.03842 ( 586) hydrogen bonds : angle 5.18130 ( 1578) link_ALPHA1-2 : bond 0.00336 ( 3) link_ALPHA1-2 : angle 2.06758 ( 9) link_ALPHA1-3 : bond 0.01037 ( 3) link_ALPHA1-3 : angle 1.75362 ( 9) link_BETA1-4 : bond 0.00248 ( 7) link_BETA1-4 : angle 2.14179 ( 21) link_NAG-ASN : bond 0.00156 ( 27) link_NAG-ASN : angle 1.39550 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6608 (tm-30) REVERT: A 264 SER cc_start: 0.8857 (t) cc_final: 0.8571 (m) REVERT: A 434 MET cc_start: 0.6650 (tmm) cc_final: 0.5957 (mtt) REVERT: C 94 GLN cc_start: 0.7414 (pm20) cc_final: 0.7150 (pm20) REVERT: D 279 ASP cc_start: 0.7499 (p0) cc_final: 0.6592 (t70) REVERT: D 435 TYR cc_start: 0.5922 (m-80) cc_final: 0.5666 (m-10) REVERT: F 539 VAL cc_start: 0.9031 (t) cc_final: 0.8654 (p) REVERT: F 629 MET cc_start: 0.7758 (mmm) cc_final: 0.7095 (mmm) REVERT: I 73 ASN cc_start: 0.8446 (t0) cc_final: 0.8190 (t0) REVERT: E 80 ASN cc_start: 0.7779 (m-40) cc_final: 0.6616 (p0) REVERT: E 99 ASN cc_start: 0.8361 (p0) cc_final: 0.8081 (p0) REVERT: E 203 GLN cc_start: 0.8723 (mt0) cc_final: 0.8231 (mp-120) REVERT: E 377 ASN cc_start: 0.8160 (t0) cc_final: 0.7812 (t0) REVERT: G 542 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7208 (ttm170) REVERT: J 61 LEU cc_start: 0.8691 (mm) cc_final: 0.8457 (mt) REVERT: J 66 ASN cc_start: 0.8357 (t0) cc_final: 0.7884 (t0) REVERT: J 82 TYR cc_start: 0.6334 (m-80) cc_final: 0.6095 (m-80) REVERT: J 86 VAL cc_start: 0.7470 (t) cc_final: 0.7055 (p) REVERT: J 94 GLN cc_start: 0.6654 (tt0) cc_final: 0.6330 (tp40) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1072 time to fit residues: 38.1353 Evaluate side-chains 162 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 169 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.116200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.102171 restraints weight = 43061.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.104566 restraints weight = 25345.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.106170 restraints weight = 16693.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.107268 restraints weight = 12230.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.107901 restraints weight = 9688.280| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14994 Z= 0.154 Angle : 0.649 13.287 20412 Z= 0.329 Chirality : 0.046 0.219 2386 Planarity : 0.004 0.062 2526 Dihedral : 5.706 54.297 2730 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -0.29 (0.21), residues: 1728 helix: 1.01 (0.27), residues: 430 sheet: 0.12 (0.28), residues: 361 loop : -0.88 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 588 TYR 0.026 0.002 TYR D 484 PHE 0.018 0.001 PHE G 522 TRP 0.049 0.002 TRP I 28 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00351 (14924) covalent geometry : angle 0.63263 (20232) SS BOND : bond 0.00339 ( 30) SS BOND : angle 1.68476 ( 60) hydrogen bonds : bond 0.03823 ( 586) hydrogen bonds : angle 5.17477 ( 1578) link_ALPHA1-2 : bond 0.00321 ( 3) link_ALPHA1-2 : angle 2.10179 ( 9) link_ALPHA1-3 : bond 0.00767 ( 3) link_ALPHA1-3 : angle 1.66516 ( 9) link_BETA1-4 : bond 0.00197 ( 7) link_BETA1-4 : angle 2.14570 ( 21) link_NAG-ASN : bond 0.00151 ( 27) link_NAG-ASN : angle 1.42157 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6714 (tm-30) REVERT: A 113 ASP cc_start: 0.8956 (t70) cc_final: 0.8675 (t0) REVERT: A 207 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7051 (tptt) REVERT: A 264 SER cc_start: 0.8783 (t) cc_final: 0.8519 (m) REVERT: A 426 MET cc_start: 0.8205 (tpp) cc_final: 0.7845 (mmm) REVERT: A 434 MET cc_start: 0.6651 (tmm) cc_final: 0.6172 (mtt) REVERT: B 629 MET cc_start: 0.7189 (mmm) cc_final: 0.6964 (tpt) REVERT: C 94 GLN cc_start: 0.7557 (pm20) cc_final: 0.7297 (pm20) REVERT: D 279 ASP cc_start: 0.7509 (p0) cc_final: 0.6588 (t70) REVERT: D 435 TYR cc_start: 0.5988 (m-80) cc_final: 0.5777 (m-10) REVERT: F 539 VAL cc_start: 0.8985 (t) cc_final: 0.8630 (p) REVERT: I 54 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7025 (mtp85) REVERT: I 60 SER cc_start: 0.9317 (p) cc_final: 0.8990 (t) REVERT: I 73 ASN cc_start: 0.8477 (t0) cc_final: 0.7386 (t0) REVERT: E 80 ASN cc_start: 0.7737 (m-40) cc_final: 0.6623 (p0) REVERT: E 99 ASN cc_start: 0.8413 (p0) cc_final: 0.8134 (p0) REVERT: E 203 GLN cc_start: 0.8715 (mt0) cc_final: 0.8239 (mp-120) REVERT: E 377 ASN cc_start: 0.8069 (t0) cc_final: 0.7796 (t0) REVERT: E 437 PRO cc_start: 0.7350 (Cg_exo) cc_final: 0.7140 (Cg_endo) REVERT: G 552 GLN cc_start: 0.6494 (tp40) cc_final: 0.6124 (mm-40) REVERT: G 626 MET cc_start: 0.7376 (ttm) cc_final: 0.6631 (mtp) REVERT: J 61 LEU cc_start: 0.8696 (mm) cc_final: 0.8446 (mm) REVERT: J 66 ASN cc_start: 0.8394 (t0) cc_final: 0.8144 (t0) REVERT: J 82 TYR cc_start: 0.6670 (m-80) cc_final: 0.6406 (m-80) REVERT: J 86 VAL cc_start: 0.7496 (t) cc_final: 0.7116 (p) REVERT: J 94 GLN cc_start: 0.6785 (tt0) cc_final: 0.6357 (tp-100) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1069 time to fit residues: 37.1490 Evaluate side-chains 168 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 86 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.112734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.098653 restraints weight = 44200.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.100941 restraints weight = 26239.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.102423 restraints weight = 17579.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.103573 restraints weight = 13100.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.104307 restraints weight = 10365.105| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14994 Z= 0.204 Angle : 0.719 10.968 20412 Z= 0.366 Chirality : 0.049 0.209 2386 Planarity : 0.005 0.065 2526 Dihedral : 6.228 55.539 2730 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.54 (0.20), residues: 1728 helix: 0.79 (0.26), residues: 422 sheet: 0.08 (0.30), residues: 339 loop : -1.05 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.038 0.003 TYR A 40 PHE 0.030 0.002 PHE G 522 TRP 0.035 0.003 TRP I 28 HIS 0.005 0.001 HIS J 27 Details of bonding type rmsd covalent geometry : bond 0.00467 (14924) covalent geometry : angle 0.69842 (20232) SS BOND : bond 0.00421 ( 30) SS BOND : angle 1.91595 ( 60) hydrogen bonds : bond 0.04107 ( 586) hydrogen bonds : angle 5.36470 ( 1578) link_ALPHA1-2 : bond 0.00286 ( 3) link_ALPHA1-2 : angle 2.26192 ( 9) link_ALPHA1-3 : bond 0.00637 ( 3) link_ALPHA1-3 : angle 2.01155 ( 9) link_BETA1-4 : bond 0.00281 ( 7) link_BETA1-4 : angle 2.45480 ( 21) link_NAG-ASN : bond 0.00252 ( 27) link_NAG-ASN : angle 1.72962 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6736 (tm-30) REVERT: A 207 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7202 (tptt) REVERT: A 264 SER cc_start: 0.8879 (t) cc_final: 0.8591 (m) REVERT: A 434 MET cc_start: 0.6474 (tmm) cc_final: 0.6146 (mtt) REVERT: B 629 MET cc_start: 0.7144 (mmm) cc_final: 0.6854 (tpt) REVERT: C 94 GLN cc_start: 0.7484 (pm20) cc_final: 0.7246 (pm20) REVERT: D 279 ASP cc_start: 0.7716 (p0) cc_final: 0.6790 (t70) REVERT: D 435 TYR cc_start: 0.6098 (m-80) cc_final: 0.5826 (m-10) REVERT: F 539 VAL cc_start: 0.9026 (t) cc_final: 0.8714 (p) REVERT: F 567 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8482 (tm-30) REVERT: F 629 MET cc_start: 0.7235 (mtp) cc_final: 0.6594 (mtp) REVERT: I 60 SER cc_start: 0.9343 (p) cc_final: 0.9069 (t) REVERT: I 73 ASN cc_start: 0.8476 (t0) cc_final: 0.7917 (t0) REVERT: E 80 ASN cc_start: 0.7764 (m-40) cc_final: 0.6514 (p0) REVERT: E 97 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8012 (mmtp) REVERT: E 99 ASN cc_start: 0.8451 (p0) cc_final: 0.8151 (p0) REVERT: E 203 GLN cc_start: 0.8742 (mt0) cc_final: 0.8289 (mp-120) REVERT: E 377 ASN cc_start: 0.8484 (t0) cc_final: 0.8273 (t0) REVERT: E 437 PRO cc_start: 0.7471 (Cg_exo) cc_final: 0.7252 (Cg_endo) REVERT: G 552 GLN cc_start: 0.6554 (tp40) cc_final: 0.6131 (mm-40) REVERT: J 82 TYR cc_start: 0.6688 (m-80) cc_final: 0.6416 (m-80) REVERT: J 86 VAL cc_start: 0.7592 (t) cc_final: 0.7227 (p) REVERT: J 94 GLN cc_start: 0.6940 (tt0) cc_final: 0.6466 (tp-100) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0967 time to fit residues: 33.3943 Evaluate side-chains 160 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 158 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS D 229 ASN D 374 HIS E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.114205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.100139 restraints weight = 43810.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.102477 restraints weight = 25818.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.104035 restraints weight = 17190.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.105153 restraints weight = 12652.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.105830 restraints weight = 10015.091| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14994 Z= 0.156 Angle : 0.673 10.522 20412 Z= 0.341 Chirality : 0.047 0.208 2386 Planarity : 0.005 0.075 2526 Dihedral : 5.975 54.026 2730 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % 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: -0.52 (0.20), residues: 1728 helix: 0.94 (0.27), residues: 421 sheet: 0.00 (0.30), residues: 331 loop : -1.06 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 54 TYR 0.024 0.002 TYR D 484 PHE 0.017 0.001 PHE B 518 TRP 0.034 0.002 TRP I 28 HIS 0.004 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00358 (14924) covalent geometry : angle 0.65490 (20232) SS BOND : bond 0.00380 ( 30) SS BOND : angle 1.71077 ( 60) hydrogen bonds : bond 0.03861 ( 586) hydrogen bonds : angle 5.24132 ( 1578) link_ALPHA1-2 : bond 0.00326 ( 3) link_ALPHA1-2 : angle 2.19669 ( 9) link_ALPHA1-3 : bond 0.00758 ( 3) link_ALPHA1-3 : angle 1.52398 ( 9) link_BETA1-4 : bond 0.00244 ( 7) link_BETA1-4 : angle 2.43761 ( 21) link_NAG-ASN : bond 0.00201 ( 27) link_NAG-ASN : angle 1.52900 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8167 (m) cc_final: 0.7807 (p) REVERT: A 80 ASN cc_start: 0.7981 (m-40) cc_final: 0.7108 (p0) REVERT: A 207 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7105 (tptt) REVERT: A 264 SER cc_start: 0.8926 (t) cc_final: 0.8610 (m) REVERT: A 426 MET cc_start: 0.8398 (tpp) cc_final: 0.8034 (mmm) REVERT: A 434 MET cc_start: 0.6434 (tmm) cc_final: 0.6231 (mtt) REVERT: C 94 GLN cc_start: 0.7440 (pm20) cc_final: 0.7219 (pm20) REVERT: D 279 ASP cc_start: 0.7712 (p0) cc_final: 0.6719 (t70) REVERT: D 435 TYR cc_start: 0.5985 (m-80) cc_final: 0.5694 (m-10) REVERT: F 539 VAL cc_start: 0.8967 (t) cc_final: 0.8618 (p) REVERT: F 567 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8371 (tm-30) REVERT: F 629 MET cc_start: 0.7411 (mtp) cc_final: 0.6724 (mtp) REVERT: I 60 SER cc_start: 0.9352 (p) cc_final: 0.9073 (t) REVERT: I 73 ASN cc_start: 0.8479 (t0) cc_final: 0.8156 (p0) REVERT: E 80 ASN cc_start: 0.7749 (m-40) cc_final: 0.7065 (p0) REVERT: E 97 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8059 (mmtp) REVERT: E 99 ASN cc_start: 0.8460 (p0) cc_final: 0.8080 (p0) REVERT: E 203 GLN cc_start: 0.8677 (mt0) cc_final: 0.8310 (mp-120) REVERT: E 377 ASN cc_start: 0.8259 (t0) cc_final: 0.7895 (t0) REVERT: E 478 ASN cc_start: 0.7980 (p0) cc_final: 0.7554 (p0) REVERT: G 530 MET cc_start: 0.7613 (mtp) cc_final: 0.7263 (mtp) REVERT: G 552 GLN cc_start: 0.6736 (tp40) cc_final: 0.6173 (mm-40) REVERT: J 82 TYR cc_start: 0.6607 (m-80) cc_final: 0.6309 (m-80) REVERT: J 86 VAL cc_start: 0.7550 (t) cc_final: 0.7183 (p) REVERT: J 94 GLN cc_start: 0.6959 (tt0) cc_final: 0.6482 (tp-100) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1018 time to fit residues: 34.4780 Evaluate side-chains 163 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 119 optimal weight: 0.0270 chunk 138 optimal weight: 0.0470 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.115696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.101767 restraints weight = 43598.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.104075 restraints weight = 25844.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.105584 restraints weight = 17242.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.106703 restraints weight = 12774.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.107370 restraints weight = 10115.186| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14994 Z= 0.132 Angle : 0.642 10.061 20412 Z= 0.327 Chirality : 0.047 0.253 2386 Planarity : 0.005 0.062 2526 Dihedral : 5.681 54.158 2730 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.52 (0.20), residues: 1728 helix: 0.86 (0.27), residues: 435 sheet: 0.08 (0.30), residues: 327 loop : -1.08 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 54 TYR 0.020 0.002 TYR D 484 PHE 0.031 0.002 PHE A 233 TRP 0.039 0.002 TRP E 96 HIS 0.006 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00301 (14924) covalent geometry : angle 0.62737 (20232) SS BOND : bond 0.00305 ( 30) SS BOND : angle 1.54070 ( 60) hydrogen bonds : bond 0.03632 ( 586) hydrogen bonds : angle 5.13342 ( 1578) link_ALPHA1-2 : bond 0.00321 ( 3) link_ALPHA1-2 : angle 2.04887 ( 9) link_ALPHA1-3 : bond 0.00750 ( 3) link_ALPHA1-3 : angle 1.31922 ( 9) link_BETA1-4 : bond 0.00254 ( 7) link_BETA1-4 : angle 2.16974 ( 21) link_NAG-ASN : bond 0.00179 ( 27) link_NAG-ASN : angle 1.40165 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8210 (m) cc_final: 0.7826 (p) REVERT: A 80 ASN cc_start: 0.7960 (m-40) cc_final: 0.7073 (p0) REVERT: A 264 SER cc_start: 0.8910 (t) cc_final: 0.8568 (m) REVERT: A 426 MET cc_start: 0.8464 (tpp) cc_final: 0.7721 (mmm) REVERT: A 434 MET cc_start: 0.6453 (tmm) cc_final: 0.6210 (mtt) REVERT: C 94 GLN cc_start: 0.7565 (pm20) cc_final: 0.7337 (pm20) REVERT: D 279 ASP cc_start: 0.7575 (p0) cc_final: 0.6483 (t70) REVERT: D 435 TYR cc_start: 0.5882 (m-80) cc_final: 0.5654 (m-10) REVERT: F 539 VAL cc_start: 0.8917 (t) cc_final: 0.8647 (p) REVERT: F 540 GLN cc_start: 0.7866 (mp10) cc_final: 0.7639 (mp10) REVERT: F 567 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8389 (tm-30) REVERT: F 629 MET cc_start: 0.7242 (mtp) cc_final: 0.6684 (mtp) REVERT: I 60 SER cc_start: 0.9344 (p) cc_final: 0.9059 (t) REVERT: I 73 ASN cc_start: 0.8433 (t0) cc_final: 0.8102 (p0) REVERT: E 80 ASN cc_start: 0.7850 (m-40) cc_final: 0.7104 (p0) REVERT: E 97 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8073 (mmtp) REVERT: E 99 ASN cc_start: 0.8498 (p0) cc_final: 0.8087 (p0) REVERT: E 203 GLN cc_start: 0.8672 (mt0) cc_final: 0.8347 (mp-120) REVERT: E 377 ASN cc_start: 0.8181 (t0) cc_final: 0.7824 (t0) REVERT: E 478 ASN cc_start: 0.7979 (p0) cc_final: 0.7670 (p0) REVERT: G 530 MET cc_start: 0.7551 (mtp) cc_final: 0.7056 (mtp) REVERT: G 552 GLN cc_start: 0.6714 (tp40) cc_final: 0.6178 (mm110) REVERT: J 82 TYR cc_start: 0.6633 (m-80) cc_final: 0.6363 (m-80) REVERT: J 86 VAL cc_start: 0.7575 (t) cc_final: 0.7213 (p) REVERT: J 94 GLN cc_start: 0.6950 (tt0) cc_final: 0.6468 (tp-100) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1090 time to fit residues: 35.8807 Evaluate side-chains 162 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 172 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 422 GLN ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.112839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.098872 restraints weight = 44260.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.101179 restraints weight = 26147.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.102569 restraints weight = 17486.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.103753 restraints weight = 13150.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.104482 restraints weight = 10422.281| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14994 Z= 0.193 Angle : 0.718 14.138 20412 Z= 0.364 Chirality : 0.048 0.204 2386 Planarity : 0.005 0.062 2526 Dihedral : 6.072 55.977 2730 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.06 % Allowed : 0.19 % Favored : 99.74 % 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: -0.66 (0.20), residues: 1728 helix: 0.75 (0.26), residues: 443 sheet: 0.07 (0.30), residues: 324 loop : -1.21 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 54 TYR 0.020 0.002 TYR D 484 PHE 0.026 0.002 PHE G 522 TRP 0.060 0.003 TRP E 112 HIS 0.006 0.001 HIS F 641 Details of bonding type rmsd covalent geometry : bond 0.00443 (14924) covalent geometry : angle 0.70074 (20232) SS BOND : bond 0.00399 ( 30) SS BOND : angle 1.72030 ( 60) hydrogen bonds : bond 0.03980 ( 586) hydrogen bonds : angle 5.24538 ( 1578) link_ALPHA1-2 : bond 0.00296 ( 3) link_ALPHA1-2 : angle 2.23539 ( 9) link_ALPHA1-3 : bond 0.00702 ( 3) link_ALPHA1-3 : angle 1.88810 ( 9) link_BETA1-4 : bond 0.00270 ( 7) link_BETA1-4 : angle 2.47901 ( 21) link_NAG-ASN : bond 0.00222 ( 27) link_NAG-ASN : angle 1.63924 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2295.43 seconds wall clock time: 40 minutes 35.13 seconds (2435.13 seconds total)