Starting phenix.real_space_refine on Sat Sep 12 08:39:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x5c_22049/09_2026/6x5c_22049.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x5c_22049/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6x5c_22049/09_2026/6x5c_22049.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x5c_22049/09_2026/6x5c_22049.cif" model { file = "/net/cci-nas-00/data/ceres_data/6x5c_22049/09_2026/6x5c_22049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x5c_22049/09_2026/6x5c_22049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x5c_22049/09_2026/6x5c_22049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x5c_22049/09_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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: 3.62, per 1000 atoms: 0.25 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: 1.61 Conformation dependent library (CDL) restraints added in 709.4 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: 0.47 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: 2.94 Time building geometry restraints manager: 2.00 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 - 17.97: 8395 17.97 - 35.93: 232 35.93 - 53.90: 72 53.90 - 71.87: 47 71.87 - 89.83: 7 Dihedral angle restraints: 8753 sinusoidal: 3635 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 8750 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.630 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 10.698 89.832 5333 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/Z covalent geometry : bond 0.02120 / 1.12 (14924) covalent geometry : angle 1.75929 / 1.15 (20232) SS BOND : bond 0.02724 / 1.27 ( 30) SS BOND : angle 3.02065 / 2.06 ( 60) hydrogen bonds : bond 0.16493 / 11.10 ( 586) hydrogen bonds : angle 8.06738 / 5.52 ( 1578) link_ALPHA1-2 : bond 0.07996 / 4.00 ( 3) link_ALPHA1-2 : angle 4.39102 / 1.98 ( 9) link_ALPHA1-3 : bond 0.05539 / 2.79 ( 3) link_ALPHA1-3 : angle 2.28801 / 1.00 ( 9) link_BETA1-4 : bond 0.06867 / 3.60 ( 7) link_BETA1-4 : angle 5.42123 / 3.23 ( 21) link_NAG-ASN : bond 0.08586 / 5.15 ( 27) link_NAG-ASN : angle 2.61349 / 1.87 ( 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 : 0.517 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: 0.1393 time to fit residues: 87.8908 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 : 0.589 ------------------------------------------------------------------------------- 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... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN E 352 GLN E 474 ASN G 652 GLN J 33 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 = 0.4365 r_free = 0.4365 target = 0.121237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.107234 restraints weight = 42748.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.109705 restraints weight = 25004.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.111377 restraints weight = 16550.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.112516 restraints weight = 12045.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.113207 restraints weight = 9441.632| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14994 Z= 0.197 Angle : 0.771 8.605 20412 Z= 0.403 Chirality : 0.049 0.204 2386 Planarity : 0.005 0.129 2526 Dihedral : 5.373 28.072 1908 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 0.26 (0.20), residues: 1728 helix: 0.95 (0.26), residues: 423 sheet: 0.33 (0.27), residues: 358 loop : -0.16 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 588 TYR 0.034 0.003 TYR D 484 PHE 0.016 0.002 PHE A 383 TRP 0.026 0.002 TRP I 28 HIS 0.008 0.002 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (14924) covalent geometry : angle 0.74811 / 0.40 (20232) SS BOND : bond 0.00604 / 0.43 ( 30) SS BOND : angle 1.37822 / 0.94 ( 60) hydrogen bonds : bond 0.05794 / 3.86 ( 586) hydrogen bonds : angle 6.13978 / 4.19 ( 1578) link_ALPHA1-2 : bond 0.00311 / 0.16 ( 3) link_ALPHA1-2 : angle 2.12512 / 1.08 ( 9) link_ALPHA1-3 : bond 0.01039 / 0.52 ( 3) link_ALPHA1-3 : angle 1.69081 / 0.90 ( 9) link_BETA1-4 : bond 0.00844 / 0.40 ( 7) link_BETA1-4 : angle 3.40612 / 2.02 ( 21) link_NAG-ASN : bond 0.00485 / 0.31 ( 27) link_NAG-ASN : angle 2.14357 / 1.41 ( 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 294 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.592 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: 0.7201 (tm-30) cc_final: 0.6465 (tm-30) REVERT: A 113 ASP cc_start: 0.8853 (t70) cc_final: 0.8605 (t0) REVERT: A 434 MET cc_start: 0.6432 (tmm) cc_final: 0.5440 (mtt) REVERT: B 629 MET cc_start: 0.7423 (mmm) cc_final: 0.7160 (tpt) REVERT: D 35 TRP cc_start: 0.6070 (m100) cc_final: 0.5845 (m100) REVERT: D 279 ASP cc_start: 0.7395 (p0) cc_final: 0.6796 (t70) REVERT: D 475 MET cc_start: 0.6984 (mmm) cc_final: 0.6455 (mmm) REVERT: F 539 VAL cc_start: 0.8911 (t) cc_final: 0.8479 (p) REVERT: I 67 PHE cc_start: 0.7974 (m-80) cc_final: 0.6970 (m-10) REVERT: I 73 ASN cc_start: 0.8354 (t0) cc_final: 0.7893 (t0) REVERT: G 570 VAL cc_start: 0.8624 (m) cc_final: 0.8294 (t) REVERT: G 618 THR cc_start: 0.7681 (p) cc_final: 0.7079 (p) REVERT: J 13 GLU cc_start: 0.5152 (tt0) cc_final: 0.4234 (pp20) REVERT: J 36 ILE cc_start: 0.8555 (mt) cc_final: 0.8243 (mp) REVERT: J 66 ASN cc_start: 0.8591 (t0) cc_final: 0.8343 (t0) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1109 time to fit residues: 50.2130 Evaluate side-chains 173 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 7.9990 chunk 28 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN C 40 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN G 640 GLN G 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.115291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.100858 restraints weight = 43585.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.103137 restraints weight = 26084.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.104687 restraints weight = 17650.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105838 restraints weight = 13104.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.106504 restraints weight = 10388.629| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14994 Z= 0.212 Angle : 0.729 8.721 20412 Z= 0.379 Chirality : 0.049 0.203 2386 Planarity : 0.005 0.115 2526 Dihedral : 5.378 25.639 1908 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % 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: -0.15 (0.20), residues: 1728 helix: 0.66 (0.26), residues: 439 sheet: 0.14 (0.27), residues: 362 loop : -0.51 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 273 TYR 0.032 0.003 TYR D 484 PHE 0.023 0.002 PHE J 43 TRP 0.030 0.002 TRP I 28 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (14924) covalent geometry : angle 0.71380 / 0.38 (20232) SS BOND : bond 0.00431 / 0.27 ( 30) SS BOND : angle 1.32433 / 0.94 ( 60) hydrogen bonds : bond 0.04648 / 3.09 ( 586) hydrogen bonds : angle 5.70001 / 3.93 ( 1578) link_ALPHA1-2 : bond 0.00320 / 0.16 ( 3) link_ALPHA1-2 : angle 2.05130 / 1.03 ( 9) link_ALPHA1-3 : bond 0.00339 / 0.17 ( 3) link_ALPHA1-3 : angle 1.45555 / 0.76 ( 9) link_BETA1-4 : bond 0.00385 / 0.22 ( 7) link_BETA1-4 : angle 2.68158 / 1.65 ( 21) link_NAG-ASN : bond 0.00312 / 0.18 ( 27) link_NAG-ASN : angle 1.70461 / 1.14 ( 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 249 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.459 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: 0.7261 (tm-30) cc_final: 0.6659 (tm-30) REVERT: A 113 ASP cc_start: 0.8882 (t70) cc_final: 0.8607 (t0) REVERT: A 434 MET cc_start: 0.6397 (tmm) cc_final: 0.5094 (mtt) REVERT: C 20 GLN cc_start: 0.8299 (mp10) cc_final: 0.8046 (mp10) REVERT: D 279 ASP cc_start: 0.7638 (p0) cc_final: 0.7033 (t70) REVERT: F 539 VAL cc_start: 0.8945 (t) cc_final: 0.8719 (p) REVERT: F 567 GLN cc_start: 0.8361 (tp40) cc_final: 0.7827 (tm-30) REVERT: I 1 LYS cc_start: 0.8677 (pttm) cc_final: 0.8269 (pttp) REVERT: I 67 PHE cc_start: 0.7983 (m-80) cc_final: 0.7362 (m-80) REVERT: I 73 ASN cc_start: 0.8517 (t0) cc_final: 0.8171 (t0) REVERT: I 94 GLN cc_start: 0.8318 (tt0) cc_final: 0.8105 (mt0) REVERT: E 95 MET cc_start: 0.6852 (ptp) cc_final: 0.5767 (ptp) REVERT: E 97 LYS cc_start: 0.8642 (mppt) cc_final: 0.8429 (mmtp) REVERT: E 99 ASN cc_start: 0.8570 (p0) cc_final: 0.8325 (p0) REVERT: E 203 GLN cc_start: 0.8646 (mt0) cc_final: 0.7742 (mp10) REVERT: G 570 VAL cc_start: 0.8561 (m) cc_final: 0.8352 (t) REVERT: G 588 ARG cc_start: 0.8152 (ptt-90) cc_final: 0.7233 (ptt90) REVERT: J 13 GLU cc_start: 0.4845 (tt0) cc_final: 0.4324 (pp20) REVERT: J 94 GLN cc_start: 0.6628 (tt0) cc_final: 0.5985 (tp40) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.1097 time to fit residues: 42.4245 Evaluate side-chains 167 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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: 0.0870 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS C 52 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 352 GLN D 374 HIS ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.119029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.105125 restraints weight = 43063.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.107568 restraints weight = 25291.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.109172 restraints weight = 16651.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.110245 restraints weight = 12148.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.111059 restraints weight = 9590.350| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4454 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= 0.128 Angle : 0.669 25.182 20412 Z= 0.342 Chirality : 0.047 0.292 2386 Planarity : 0.005 0.092 2526 Dihedral : 5.139 28.774 1908 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.13 % Allowed : 2.05 % Favored : 97.83 % 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: -0.01 (0.20), residues: 1728 helix: 0.98 (0.27), residues: 430 sheet: 0.17 (0.28), residues: 352 loop : -0.50 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 419 TYR 0.030 0.002 TYR D 484 PHE 0.013 0.001 PHE J 43 TRP 0.047 0.002 TRP I 28 HIS 0.008 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (14924) covalent geometry : angle 0.64808 / 0.34 (20232) SS BOND : bond 0.00622 / 0.42 ( 30) SS BOND : angle 2.34869 / 1.73 ( 60) hydrogen bonds : bond 0.04106 / 2.73 ( 586) hydrogen bonds : angle 5.34473 / 3.71 ( 1578) link_ALPHA1-2 : bond 0.00480 / 0.24 ( 3) link_ALPHA1-2 : angle 1.79057 / 0.89 ( 9) link_ALPHA1-3 : bond 0.00532 / 0.26 ( 3) link_ALPHA1-3 : angle 1.32958 / 0.70 ( 9) link_BETA1-4 : bond 0.00416 / 0.23 ( 7) link_BETA1-4 : angle 2.16930 / 1.35 ( 21) link_NAG-ASN : bond 0.00267 / 0.15 ( 27) link_NAG-ASN : angle 1.46484 / 0.94 ( 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 240 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 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: A 64 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6567 (tm-30) REVERT: A 434 MET cc_start: 0.6591 (tmm) cc_final: 0.5551 (mtt) REVERT: B 629 MET cc_start: 0.7642 (mmm) cc_final: 0.7289 (tpt) REVERT: D 279 ASP cc_start: 0.7441 (p0) cc_final: 0.6661 (t70) REVERT: D 435 TYR cc_start: 0.5909 (m-80) cc_final: 0.5705 (m-80) REVERT: F 539 VAL cc_start: 0.8911 (t) cc_final: 0.8566 (p) REVERT: F 626 MET cc_start: 0.8019 (ttm) cc_final: 0.7793 (mtp) REVERT: I 34 ILE cc_start: 0.7935 (mm) cc_final: 0.7591 (mm) REVERT: I 67 PHE cc_start: 0.7915 (m-80) cc_final: 0.7409 (m-80) REVERT: I 73 ASN cc_start: 0.8385 (t0) cc_final: 0.7992 (t0) REVERT: E 99 ASN cc_start: 0.8456 (p0) cc_final: 0.8162 (p0) REVERT: E 203 GLN cc_start: 0.8680 (mt0) cc_final: 0.8089 (mp-120) REVERT: G 565 MET cc_start: 0.7669 (ttt) cc_final: 0.7449 (ttm) REVERT: G 588 ARG cc_start: 0.7962 (ptt-90) cc_final: 0.7419 (ptt90) REVERT: G 629 MET cc_start: 0.7642 (mpp) cc_final: 0.6861 (mpp) REVERT: J 66 ASN cc_start: 0.8824 (t0) cc_final: 0.8466 (t0) REVERT: J 94 GLN cc_start: 0.6717 (tt0) cc_final: 0.6184 (tp40) outliers start: 2 outliers final: 0 residues processed: 238 average time/residue: 0.1115 time to fit residues: 40.8898 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 : 0.559 ------------------------------------------------------------------------------- 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: 20.0000 chunk 90 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 562 GLN B 656 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.118897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.104866 restraints weight = 42917.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.107306 restraints weight = 25224.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.108914 restraints weight = 16604.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.110059 restraints weight = 12113.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.110727 restraints weight = 9500.711| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14994 Z= 0.126 Angle : 0.627 14.166 20412 Z= 0.322 Chirality : 0.045 0.198 2386 Planarity : 0.004 0.074 2526 Dihedral : 4.971 30.750 1908 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.06 % Allowed : 1.47 % Favored : 98.47 % 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: -0.02 (0.21), residues: 1728 helix: 1.01 (0.26), residues: 435 sheet: 0.21 (0.28), residues: 355 loop : -0.55 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 476 TYR 0.028 0.002 TYR D 484 PHE 0.012 0.001 PHE A 233 TRP 0.032 0.001 TRP I 28 HIS 0.005 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (14924) covalent geometry : angle 0.60816 / 0.32 (20232) SS BOND : bond 0.00282 / 0.19 ( 30) SS BOND : angle 2.20781 / 1.66 ( 60) hydrogen bonds : bond 0.03788 / 2.49 ( 586) hydrogen bonds : angle 5.23202 / 3.67 ( 1578) link_ALPHA1-2 : bond 0.00409 / 0.21 ( 3) link_ALPHA1-2 : angle 1.81785 / 0.91 ( 9) link_ALPHA1-3 : bond 0.00496 / 0.25 ( 3) link_ALPHA1-3 : angle 1.24181 / 0.64 ( 9) link_BETA1-4 : bond 0.00361 / 0.21 ( 7) link_BETA1-4 : angle 2.07229 / 1.27 ( 21) link_NAG-ASN : bond 0.00184 / 0.11 ( 27) link_NAG-ASN : angle 1.22443 / 0.82 ( 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 229 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.580 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: A 64 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6522 (tm-30) REVERT: A 434 MET cc_start: 0.6671 (tmm) cc_final: 0.6070 (mtt) REVERT: D 279 ASP cc_start: 0.7438 (p0) cc_final: 0.6593 (t70) REVERT: F 539 VAL cc_start: 0.8966 (t) cc_final: 0.8589 (p) REVERT: F 626 MET cc_start: 0.8155 (ttm) cc_final: 0.7857 (mtp) REVERT: I 67 PHE cc_start: 0.7959 (m-80) cc_final: 0.7444 (m-80) REVERT: I 73 ASN cc_start: 0.8340 (t0) cc_final: 0.7909 (t0) REVERT: E 99 ASN cc_start: 0.8422 (p0) cc_final: 0.8081 (p0) REVERT: E 203 GLN cc_start: 0.8618 (mt0) cc_final: 0.8101 (mp-120) REVERT: E 377 ASN cc_start: 0.8242 (t0) cc_final: 0.7891 (t0) REVERT: G 588 ARG cc_start: 0.8092 (ptt-90) cc_final: 0.7515 (ptt90) REVERT: J 66 ASN cc_start: 0.8847 (t0) cc_final: 0.8459 (t0) REVERT: J 94 GLN cc_start: 0.6627 (tt0) cc_final: 0.6213 (tp40) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1106 time to fit residues: 38.9745 Evaluate side-chains 157 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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: 4.9990 chunk 94 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN E 103 GLN G 540 GLN J 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.111055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.096850 restraints weight = 44585.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.099155 restraints weight = 26539.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.100691 restraints weight = 17845.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.101773 restraints weight = 13258.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.102447 restraints weight = 10599.794| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14994 Z= 0.279 Angle : 0.804 12.024 20412 Z= 0.413 Chirality : 0.051 0.228 2386 Planarity : 0.005 0.066 2526 Dihedral : 5.594 30.792 1908 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.06 % Allowed : 1.79 % Favored : 98.15 % 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: -0.58 (0.20), residues: 1728 helix: 0.54 (0.26), residues: 431 sheet: 0.06 (0.29), residues: 353 loop : -0.99 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 273 TYR 0.038 0.004 TYR A 40 PHE 0.035 0.003 PHE G 522 TRP 0.057 0.003 TRP D 112 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.28 (14924) covalent geometry : angle 0.78131 / 0.41 (20232) SS BOND : bond 0.00608 / 0.43 ( 30) SS BOND : angle 2.29316 / 1.69 ( 60) hydrogen bonds : bond 0.04699 / 3.12 ( 586) hydrogen bonds : angle 5.60038 / 3.96 ( 1578) link_ALPHA1-2 : bond 0.00167 / 0.08 ( 3) link_ALPHA1-2 : angle 2.21608 / 1.12 ( 9) link_ALPHA1-3 : bond 0.00370 / 0.19 ( 3) link_ALPHA1-3 : angle 1.70756 / 0.88 ( 9) link_BETA1-4 : bond 0.00353 / 0.18 ( 7) link_BETA1-4 : angle 2.92988 / 1.73 ( 21) link_NAG-ASN : bond 0.00368 / 0.21 ( 27) link_NAG-ASN : angle 1.88027 / 1.25 ( 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 213 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6749 (tm-30) REVERT: A 113 ASP cc_start: 0.9050 (t70) cc_final: 0.8779 (t0) REVERT: A 264 SER cc_start: 0.8908 (t) cc_final: 0.8672 (m) REVERT: A 434 MET cc_start: 0.6899 (tmm) cc_final: 0.6164 (mtt) REVERT: D 279 ASP cc_start: 0.7854 (p0) cc_final: 0.7000 (t0) REVERT: F 567 GLN cc_start: 0.8379 (tp40) cc_final: 0.8106 (tm-30) REVERT: F 573 ILE cc_start: 0.8100 (mm) cc_final: 0.7888 (mm) REVERT: I 60 SER cc_start: 0.9353 (p) cc_final: 0.9066 (t) REVERT: I 67 PHE cc_start: 0.8100 (m-80) cc_final: 0.7414 (m-80) REVERT: I 73 ASN cc_start: 0.8492 (t0) cc_final: 0.8036 (t0) REVERT: E 80 ASN cc_start: 0.7770 (m-40) cc_final: 0.6768 (p0) REVERT: E 95 MET cc_start: 0.6602 (ptp) cc_final: 0.6034 (ptp) REVERT: E 99 ASN cc_start: 0.8444 (p0) cc_final: 0.8195 (p0) REVERT: E 203 GLN cc_start: 0.8744 (mt0) cc_final: 0.8220 (mp-120) REVERT: E 435 TYR cc_start: 0.6740 (m-80) cc_final: 0.6329 (m-10) REVERT: E 478 ASN cc_start: 0.8122 (p0) cc_final: 0.7725 (p0) REVERT: J 66 ASN cc_start: 0.8947 (t0) cc_final: 0.8673 (t0) REVERT: J 86 VAL cc_start: 0.7423 (t) cc_final: 0.7064 (p) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.1015 time to fit residues: 34.3063 Evaluate side-chains 158 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN D 374 HIS ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN G 540 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.114593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.100558 restraints weight = 43771.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.102840 restraints weight = 25843.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.104429 restraints weight = 17357.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.105544 restraints weight = 12788.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.106315 restraints weight = 10129.321| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14994 Z= 0.145 Angle : 0.667 12.567 20412 Z= 0.340 Chirality : 0.047 0.209 2386 Planarity : 0.005 0.066 2526 Dihedral : 5.253 32.031 1908 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.13 % Allowed : 1.09 % Favored : 98.79 % 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: -0.42 (0.20), residues: 1728 helix: 0.89 (0.27), residues: 425 sheet: 0.04 (0.28), residues: 366 loop : -0.95 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 588 TYR 0.026 0.002 TYR D 484 PHE 0.017 0.002 PHE A 233 TRP 0.067 0.002 TRP I 28 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (14924) covalent geometry : angle 0.64710 / 0.33 (20232) SS BOND : bond 0.00379 / 0.26 ( 30) SS BOND : angle 2.12353 / 1.59 ( 60) hydrogen bonds : bond 0.03943 / 2.62 ( 586) hydrogen bonds : angle 5.29284 / 3.75 ( 1578) link_ALPHA1-2 : bond 0.00410 / 0.21 ( 3) link_ALPHA1-2 : angle 1.96113 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00554 / 0.29 ( 3) link_ALPHA1-3 : angle 1.30527 / 0.66 ( 9) link_BETA1-4 : bond 0.00276 / 0.14 ( 7) link_BETA1-4 : angle 2.56040 / 1.66 ( 21) link_NAG-ASN : bond 0.00202 / 0.13 ( 27) link_NAG-ASN : angle 1.42193 / 0.94 ( 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 219 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.587 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: 0.7181 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 264 SER cc_start: 0.8843 (t) cc_final: 0.8570 (m) REVERT: A 434 MET cc_start: 0.6599 (tmm) cc_final: 0.6106 (mtt) REVERT: D 279 ASP cc_start: 0.7657 (p0) cc_final: 0.6736 (t70) REVERT: F 539 VAL cc_start: 0.8972 (t) cc_final: 0.8709 (p) REVERT: F 626 MET cc_start: 0.8130 (ttm) cc_final: 0.7880 (mtp) REVERT: F 629 MET cc_start: 0.7418 (mtp) cc_final: 0.7112 (mtp) REVERT: I 60 SER cc_start: 0.9333 (p) cc_final: 0.9014 (t) REVERT: I 73 ASN cc_start: 0.8375 (t0) cc_final: 0.7922 (t0) REVERT: E 80 ASN cc_start: 0.7813 (m-40) cc_final: 0.6811 (p0) REVERT: E 97 LYS cc_start: 0.8618 (mppt) cc_final: 0.8085 (mmtm) REVERT: E 99 ASN cc_start: 0.8432 (p0) cc_final: 0.8067 (p0) REVERT: E 203 GLN cc_start: 0.8676 (mt0) cc_final: 0.8243 (mp-120) REVERT: E 377 ASN cc_start: 0.8331 (t0) cc_final: 0.8071 (t0) REVERT: E 435 TYR cc_start: 0.6618 (m-80) cc_final: 0.6140 (m-10) REVERT: E 437 PRO cc_start: 0.7139 (Cg_exo) cc_final: 0.6938 (Cg_endo) REVERT: E 478 ASN cc_start: 0.8056 (p0) cc_final: 0.7752 (p0) REVERT: J 66 ASN cc_start: 0.8876 (t0) cc_final: 0.8430 (t0) REVERT: J 86 VAL cc_start: 0.7482 (t) cc_final: 0.7123 (p) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.1030 time to fit residues: 35.6833 Evaluate side-chains 158 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 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: 10.0000 chunk 172 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 0.0020 chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.113220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.099068 restraints weight = 44233.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.101378 restraints weight = 26266.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.102929 restraints weight = 17569.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.104041 restraints weight = 12984.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.104792 restraints weight = 10324.479| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14994 Z= 0.177 Angle : 0.689 10.479 20412 Z= 0.351 Chirality : 0.048 0.335 2386 Planarity : 0.005 0.065 2526 Dihedral : 5.265 29.782 1908 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.51 (0.20), residues: 1728 helix: 0.85 (0.26), residues: 432 sheet: 0.05 (0.30), residues: 347 loop : -1.05 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 588 TYR 0.028 0.002 TYR D 484 PHE 0.024 0.002 PHE G 522 TRP 0.046 0.002 TRP I 28 HIS 0.004 0.001 HIS I 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (14924) covalent geometry : angle 0.66721 / 0.34 (20232) SS BOND : bond 0.00390 / 0.27 ( 30) SS BOND : angle 1.91479 / 1.41 ( 60) hydrogen bonds : bond 0.03976 / 2.65 ( 586) hydrogen bonds : angle 5.31989 / 3.77 ( 1578) link_ALPHA1-2 : bond 0.00268 / 0.14 ( 3) link_ALPHA1-2 : angle 1.98834 / 1.01 ( 9) link_ALPHA1-3 : bond 0.00383 / 0.20 ( 3) link_ALPHA1-3 : angle 1.45385 / 0.74 ( 9) link_BETA1-4 : bond 0.00298 / 0.15 ( 7) link_BETA1-4 : angle 2.59428 / 1.60 ( 21) link_NAG-ASN : bond 0.00237 / 0.13 ( 27) link_NAG-ASN : angle 1.82197 / 1.16 ( 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 209 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.679 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 264 SER cc_start: 0.8908 (t) cc_final: 0.8568 (m) REVERT: A 434 MET cc_start: 0.6660 (tmm) cc_final: 0.6137 (mtt) REVERT: B 626 MET cc_start: 0.6585 (ttm) cc_final: 0.6377 (ttt) REVERT: D 279 ASP cc_start: 0.7727 (p0) cc_final: 0.6856 (t70) REVERT: D 435 TYR cc_start: 0.5986 (m-80) cc_final: 0.5748 (m-10) REVERT: F 539 VAL cc_start: 0.8993 (t) cc_final: 0.8713 (p) REVERT: F 567 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8585 (tm-30) REVERT: F 626 MET cc_start: 0.8203 (ttm) cc_final: 0.7876 (mtp) REVERT: I 60 SER cc_start: 0.9354 (p) cc_final: 0.9050 (t) REVERT: I 73 ASN cc_start: 0.8415 (t0) cc_final: 0.7996 (t0) REVERT: E 80 ASN cc_start: 0.7780 (m-40) cc_final: 0.7009 (p0) REVERT: E 97 LYS cc_start: 0.8579 (mppt) cc_final: 0.8066 (mmtm) REVERT: E 99 ASN cc_start: 0.8360 (p0) cc_final: 0.8003 (p0) REVERT: E 203 GLN cc_start: 0.8666 (mt0) cc_final: 0.8349 (mp-120) REVERT: E 377 ASN cc_start: 0.8290 (t0) cc_final: 0.8043 (t0) REVERT: E 435 TYR cc_start: 0.6614 (m-80) cc_final: 0.6125 (m-10) REVERT: E 478 ASN cc_start: 0.7874 (p0) cc_final: 0.7526 (p0) REVERT: J 61 LEU cc_start: 0.9000 (mm) cc_final: 0.8548 (mm) REVERT: J 66 ASN cc_start: 0.8856 (t0) cc_final: 0.8633 (t0) REVERT: J 86 VAL cc_start: 0.7529 (t) cc_final: 0.7183 (p) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1021 time to fit residues: 33.9299 Evaluate side-chains 154 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 0.4980 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 0.0060 chunk 49 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.114056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.100054 restraints weight = 44264.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.102378 restraints weight = 26050.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.103961 restraints weight = 17351.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.105081 restraints weight = 12735.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105740 restraints weight = 10096.068| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14994 Z= 0.153 Angle : 0.655 9.381 20412 Z= 0.335 Chirality : 0.047 0.272 2386 Planarity : 0.005 0.064 2526 Dihedral : 5.180 29.827 1908 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.13 % Allowed : 0.45 % Favored : 99.42 % 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: -0.49 (0.20), residues: 1728 helix: 0.95 (0.27), residues: 432 sheet: -0.01 (0.29), residues: 363 loop : -1.06 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 480 TYR 0.025 0.002 TYR D 484 PHE 0.028 0.002 PHE A 233 TRP 0.042 0.002 TRP I 28 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14924) covalent geometry : angle 0.63676 / 0.33 (20232) SS BOND : bond 0.00335 / 0.23 ( 30) SS BOND : angle 1.76236 / 1.29 ( 60) hydrogen bonds : bond 0.03821 / 2.55 ( 586) hydrogen bonds : angle 5.24296 / 3.73 ( 1578) link_ALPHA1-2 : bond 0.00336 / 0.17 ( 3) link_ALPHA1-2 : angle 1.97470 / 1.00 ( 9) link_ALPHA1-3 : bond 0.00421 / 0.22 ( 3) link_ALPHA1-3 : angle 1.35371 / 0.69 ( 9) link_BETA1-4 : bond 0.00291 / 0.15 ( 7) link_BETA1-4 : angle 2.45334 / 1.52 ( 21) link_NAG-ASN : bond 0.00180 / 0.11 ( 27) link_NAG-ASN : angle 1.56051 / 1.01 ( 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 213 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 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 51 THR cc_start: 0.8144 (m) cc_final: 0.7774 (p) REVERT: A 80 ASN cc_start: 0.7971 (m-40) cc_final: 0.7078 (p0) REVERT: A 264 SER cc_start: 0.8937 (t) cc_final: 0.8607 (m) REVERT: A 368 ASP cc_start: 0.7577 (t70) cc_final: 0.5704 (t0) REVERT: A 434 MET cc_start: 0.6562 (tmm) cc_final: 0.6148 (mtt) REVERT: B 626 MET cc_start: 0.6539 (ttm) cc_final: 0.6325 (ttt) REVERT: D 279 ASP cc_start: 0.7723 (p0) cc_final: 0.6764 (t70) REVERT: D 435 TYR cc_start: 0.5868 (m-80) cc_final: 0.5633 (m-10) REVERT: F 539 VAL cc_start: 0.8960 (t) cc_final: 0.8644 (p) REVERT: F 565 MET cc_start: 0.6599 (mmm) cc_final: 0.6321 (tpt) REVERT: F 567 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8556 (tm-30) REVERT: F 626 MET cc_start: 0.8197 (ttm) cc_final: 0.7853 (mtp) REVERT: I 54 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7275 (mtp85) REVERT: I 60 SER cc_start: 0.9345 (p) cc_final: 0.9050 (t) REVERT: I 73 ASN cc_start: 0.8365 (t0) cc_final: 0.7261 (t0) REVERT: E 80 ASN cc_start: 0.7840 (m-40) cc_final: 0.7111 (p0) REVERT: E 97 LYS cc_start: 0.8583 (mppt) cc_final: 0.8084 (mmtm) REVERT: E 99 ASN cc_start: 0.8345 (p0) cc_final: 0.7950 (p0) REVERT: E 203 GLN cc_start: 0.8623 (mt0) cc_final: 0.8358 (mp-120) REVERT: E 377 ASN cc_start: 0.8200 (t0) cc_final: 0.7923 (t0) REVERT: E 435 TYR cc_start: 0.6448 (m-80) cc_final: 0.6054 (m-80) REVERT: E 478 ASN cc_start: 0.7969 (p0) cc_final: 0.7489 (p0) REVERT: G 530 MET cc_start: 0.7604 (mtp) cc_final: 0.7298 (mtp) REVERT: J 66 ASN cc_start: 0.8858 (t0) cc_final: 0.8628 (t0) REVERT: J 86 VAL cc_start: 0.7574 (t) cc_final: 0.7223 (p) outliers start: 2 outliers final: 0 residues processed: 213 average time/residue: 0.1032 time to fit residues: 34.7273 Evaluate side-chains 158 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 59 optimal weight: 0.4980 chunk 67 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN E 80 ASN E 105 HIS G 540 GLN G 552 GLN J 32 ASN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.110510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.096241 restraints weight = 45159.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.098406 restraints weight = 27276.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.099858 restraints weight = 18784.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.100884 restraints weight = 14199.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.101522 restraints weight = 11481.535| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14994 Z= 0.245 Angle : 0.774 9.812 20412 Z= 0.394 Chirality : 0.050 0.255 2386 Planarity : 0.005 0.070 2526 Dihedral : 5.644 29.005 1908 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % 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: -0.92 (0.20), residues: 1728 helix: 0.35 (0.25), residues: 451 sheet: -0.18 (0.29), residues: 367 loop : -1.29 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 476 TYR 0.025 0.003 TYR D 484 PHE 0.038 0.003 PHE G 522 TRP 0.043 0.003 TRP E 45 HIS 0.007 0.002 HIS J 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (14924) covalent geometry : angle 0.75180 / 0.39 (20232) SS BOND : bond 0.00478 / 0.33 ( 30) SS BOND : angle 2.01434 / 1.46 ( 60) hydrogen bonds : bond 0.04447 / 2.97 ( 586) hydrogen bonds : angle 5.60260 / 3.97 ( 1578) link_ALPHA1-2 : bond 0.00209 / 0.11 ( 3) link_ALPHA1-2 : angle 2.24535 / 1.14 ( 9) link_ALPHA1-3 : bond 0.00357 / 0.18 ( 3) link_ALPHA1-3 : angle 1.63013 / 0.85 ( 9) link_BETA1-4 : bond 0.00438 / 0.21 ( 7) link_BETA1-4 : angle 2.90512 / 1.74 ( 21) link_NAG-ASN : bond 0.00313 / 0.19 ( 27) link_NAG-ASN : angle 1.97021 / 1.27 ( 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 209 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8234 (m) cc_final: 0.7862 (p) REVERT: A 80 ASN cc_start: 0.8067 (m-40) cc_final: 0.7147 (p0) REVERT: A 264 SER cc_start: 0.8989 (t) cc_final: 0.8660 (m) REVERT: A 434 MET cc_start: 0.6780 (tmm) cc_final: 0.6212 (mtt) REVERT: B 626 MET cc_start: 0.6874 (ttm) cc_final: 0.6509 (ttm) REVERT: D 95 MET cc_start: 0.7723 (ptp) cc_final: 0.7295 (ptp) REVERT: F 539 VAL cc_start: 0.9002 (t) cc_final: 0.8692 (p) REVERT: F 567 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8479 (tm-30) REVERT: F 626 MET cc_start: 0.8015 (ttm) cc_final: 0.7581 (mtp) REVERT: I 60 SER cc_start: 0.9366 (p) cc_final: 0.9114 (t) REVERT: I 73 ASN cc_start: 0.8384 (t0) cc_final: 0.7819 (t0) REVERT: E 80 ASN cc_start: 0.7866 (m110) cc_final: 0.7355 (p0) REVERT: E 97 LYS cc_start: 0.8562 (mppt) cc_final: 0.7930 (mmtm) REVERT: E 99 ASN cc_start: 0.8378 (p0) cc_final: 0.8125 (p0) REVERT: E 203 GLN cc_start: 0.8773 (mt0) cc_final: 0.8358 (mp-120) REVERT: E 377 ASN cc_start: 0.8280 (t0) cc_final: 0.8068 (t0) REVERT: E 478 ASN cc_start: 0.7939 (p0) cc_final: 0.7700 (p0) REVERT: G 530 MET cc_start: 0.7745 (mtp) cc_final: 0.7268 (mtp) REVERT: J 61 LEU cc_start: 0.8961 (mm) cc_final: 0.8429 (mm) REVERT: J 86 VAL cc_start: 0.7558 (t) cc_final: 0.7200 (p) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1100 time to fit residues: 36.1830 Evaluate side-chains 148 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 8.9990 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 105 HIS G 652 GLN G 656 ASN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.112611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.098493 restraints weight = 44618.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.100750 restraints weight = 26766.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.102274 restraints weight = 18086.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.103192 restraints weight = 13518.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.103986 restraints weight = 11011.121| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14994 Z= 0.168 Angle : 0.699 9.070 20412 Z= 0.356 Chirality : 0.048 0.288 2386 Planarity : 0.005 0.069 2526 Dihedral : 5.457 29.165 1908 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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: -0.81 (0.20), residues: 1728 helix: 0.52 (0.26), residues: 449 sheet: -0.20 (0.29), residues: 351 loop : -1.21 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 588 TYR 0.023 0.002 TYR D 484 PHE 0.030 0.002 PHE A 233 TRP 0.079 0.002 TRP I 28 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (14924) covalent geometry : angle 0.67895 / 0.35 (20232) SS BOND : bond 0.00383 / 0.26 ( 30) SS BOND : angle 1.82363 / 1.32 ( 60) hydrogen bonds : bond 0.04115 / 2.74 ( 586) hydrogen bonds : angle 5.41689 / 3.85 ( 1578) link_ALPHA1-2 : bond 0.00285 / 0.14 ( 3) link_ALPHA1-2 : angle 2.11864 / 1.07 ( 9) link_ALPHA1-3 : bond 0.00426 / 0.22 ( 3) link_ALPHA1-3 : angle 1.38522 / 0.70 ( 9) link_BETA1-4 : bond 0.00348 / 0.17 ( 7) link_BETA1-4 : angle 2.57038 / 1.56 ( 21) link_NAG-ASN : bond 0.00201 / 0.13 ( 27) link_NAG-ASN : angle 1.72265 / 1.10 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.08 seconds wall clock time: 42 minutes 27.37 seconds (2547.37 seconds total)