Starting phenix.real_space_refine on Thu Sep 18 07:44:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ni9_49457/09_2025/9ni9_49457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ni9_49457/09_2025/9ni9_49457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ni9_49457/09_2025/9ni9_49457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ni9_49457/09_2025/9ni9_49457.map" model { file = "/net/cci-nas-00/data/ceres_data/9ni9_49457/09_2025/9ni9_49457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ni9_49457/09_2025/9ni9_49457.cif" } resolution = 3.8 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= -0.001 sd= 0.026 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 103 5.16 5 C 9325 2.51 5 N 2529 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14956 Number of models: 1 Model: "" Number of chains: 19 Chain: "H" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 630 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "L" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 542 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'UNK:plan-1': 101} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3376 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 3 Chain: "D" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "A" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3390 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 3 Chain: "B" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 931 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "E" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3365 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 3 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 982 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.24 Number of scatterers: 14956 At special positions: 0 Unit cell: (119.6, 127.65, 149.5, 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 103 16.00 O 2999 8.00 N 2529 7.00 C 9325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.02 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS B 663 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 663 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 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 F 663 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 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=2.03 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 F 598 " - pdb=" SG CYS F 604 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " NAG J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " NAG M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 230 " " NAG A 606 " - " ASN A 289 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 442 " " NAG A 611 " - " ASN A 448 " " NAG A 612 " - " ASN A 88 " " NAG A 613 " - " ASN A 133 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 230 " " NAG C 606 " - " ASN C 289 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 332 " " NAG C 609 " - " ASN C 386 " " NAG C 610 " - " ASN C 442 " " NAG C 611 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG D 703 " - " ASN D 656 " " NAG E 601 " - " ASN E 130 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 230 " " NAG E 606 " - " ASN E 289 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 332 " " NAG E 609 " - " ASN E 442 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 88 " " NAG E 612 " - " ASN E 392 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN C 241 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN E 241 " " NAG N 1 " - " ASN E 262 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 587.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 32 sheets defined 25.2% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'H' and resid 62 through 66 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.032A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 339 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.740A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 657 removed outlier: 4.336A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.566A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.150A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.517A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.923A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.989A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.479A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.537A pdb=" N ASP F 632 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS F 633 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 660 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.608A pdb=" N UNK H 84 " --> pdb=" O UNK H 18 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N UNK H 20 " --> pdb=" O UNK H 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.642A pdb=" N UNK H 58 " --> pdb=" O UNK H 53 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N UNK H 48 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N UNK H 39 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N UNK H 36 " --> pdb=" O UNK H 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AA4, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.769A pdb=" N UNK L 32 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N UNK L 84 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N UNK L 85 " --> pdb=" O UNK L 100 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N UNK L 100 " --> pdb=" O UNK L 85 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS L 87 " --> pdb=" O UNK L 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.240A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB1, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AB2, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.725A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.824A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 301 through 307 removed outlier: 3.864A pdb=" N GLN C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR C 320 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 334 Processing sheet with id=AB5, first strand: chain 'C' and resid 393 through 394 removed outlier: 6.570A pdb=" N THR C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.059A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.371A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.526A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 283 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 283 through 287 current: chain 'A' and resid 331 through 334 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 331 through 334 current: chain 'A' and resid 465 through 469 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 300 through 312 removed outlier: 6.431A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 374 through 377 removed outlier: 4.518A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 494 through 499 Processing sheet with id=AC8, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.496A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AD2, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AD3, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD4, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.738A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 260 current: chain 'E' and resid 284 through 312 removed outlier: 6.342A pdb=" N GLY E 324 " --> pdb=" O PRO E 299 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 324 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 467 through 470 488 hydrogen bonds defined for protein. 1287 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: 2.41 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4225 1.33 - 1.48: 4602 1.48 - 1.63: 6268 1.63 - 1.77: 36 1.77 - 1.92: 99 Bond restraints: 15230 Sorted by residual: bond pdb=" NE ARG C 504 " pdb=" CZ ARG C 504 " ideal model delta sigma weight residual 1.326 1.408 -0.082 1.10e-02 8.26e+03 5.52e+01 bond pdb=" CZ2 TRP A 395 " pdb=" CH2 TRP A 395 " ideal model delta sigma weight residual 1.368 1.480 -0.112 1.90e-02 2.77e+03 3.45e+01 bond pdb=" CZ2 TRP E 395 " pdb=" CH2 TRP E 395 " ideal model delta sigma weight residual 1.368 1.477 -0.109 1.90e-02 2.77e+03 3.30e+01 bond pdb=" CZ2 TRP C 395 " pdb=" CH2 TRP C 395 " ideal model delta sigma weight residual 1.368 1.477 -0.109 1.90e-02 2.77e+03 3.26e+01 bond pdb=" CD2 TRP A 395 " pdb=" CE3 TRP A 395 " ideal model delta sigma weight residual 1.398 1.488 -0.090 1.60e-02 3.91e+03 3.16e+01 ... (remaining 15225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 17364 2.17 - 4.35: 2801 4.35 - 6.52: 508 6.52 - 8.70: 63 8.70 - 10.87: 7 Bond angle restraints: 20743 Sorted by residual: angle pdb=" N GLU A 370 " pdb=" CA GLU A 370 " pdb=" C GLU A 370 " ideal model delta sigma weight residual 114.62 103.75 10.87 1.14e+00 7.69e-01 9.10e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 127.82 -8.26 1.02e+00 9.61e-01 6.55e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.02e+00 9.61e-01 6.10e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 125.19 -5.53 7.30e-01 1.88e+00 5.74e+01 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 108.45 99.64 8.81 1.20e+00 6.94e-01 5.39e+01 ... (remaining 20738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 9650 23.39 - 46.78: 155 46.78 - 70.18: 52 70.18 - 93.57: 34 93.57 - 116.96: 13 Dihedral angle restraints: 9904 sinusoidal: 4459 harmonic: 5445 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 166.70 -73.70 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS B 663 " pdb=" CB CYS B 663 " ideal model delta sinusoidal sigma weight residual 93.00 142.82 -49.82 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.25 39.25 1 1.00e+01 1.00e-02 2.17e+01 ... (remaining 9901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 2174 0.171 - 0.341: 301 0.341 - 0.512: 91 0.512 - 0.682: 0 0.682 - 0.853: 1 Chirality restraints: 2567 Sorted by residual: chirality pdb=" C1 NAG G 3 " pdb=" O4 NAG G 2 " pdb=" C2 NAG G 3 " pdb=" O5 NAG G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 ... (remaining 2564 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 611 " -0.223 2.00e-02 2.50e+03 1.84e-01 4.24e+02 pdb=" C7 NAG A 611 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG A 611 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG A 611 " 0.301 2.00e-02 2.50e+03 pdb=" O7 NAG A 611 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 604 " -0.135 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG A 604 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 604 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG A 604 " 0.178 2.00e-02 2.50e+03 pdb=" O7 NAG A 604 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 442 " 0.086 2.00e-02 2.50e+03 9.24e-02 1.07e+02 pdb=" CG ASN A 442 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 442 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 442 " -0.145 2.00e-02 2.50e+03 pdb=" C1 NAG A 610 " 0.112 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1524 2.72 - 3.26: 14099 3.26 - 3.81: 23301 3.81 - 4.35: 30012 4.35 - 4.90: 47870 Nonbonded interactions: 116806 Sorted by model distance: nonbonded pdb=" OG1 THR C 373 " pdb=" O CYS C 385 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.264 3.040 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.361 2.496 nonbonded pdb=" OG1 THR A 373 " pdb=" O CYS A 385 " model vdw 2.365 3.040 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.377 3.120 ... (remaining 116801 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 32 through 503 or resid 603 through 613)) selection = (chain 'C' and (resid 32 through 503 or resid 601 through 611)) selection = (chain 'E' and (resid 32 through 503 or resid 602 through 612)) } ncs_group { reference = (chain 'B' and resid 525 through 664) selection = (chain 'D' and (resid 525 through 539 or resid 568 through 664)) selection = (chain 'F' and (resid 525 through 539 or resid 568 through 664)) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) } ncs_group { reference = (chain 'H' and (resid 1 through 33 or resid 37 through 89 or resid 97 through 10 \ 6 or resid 108 through 111 or resid 119 through 122)) selection = (chain 'L' and (resid 1 through 96 or resid 98 through 105)) } 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: 0.010 Normalize map: mean=0, sd=1: 6.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.680 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.021 0.127 15322 Z= 1.128 Angle : 1.729 19.472 20984 Z= 1.097 Chirality : 0.134 0.853 2567 Planarity : 0.010 0.184 2585 Dihedral : 11.710 116.962 6255 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.20), residues: 1616 helix: -0.10 (0.24), residues: 395 sheet: 0.59 (0.23), residues: 433 loop : -0.05 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 308 TYR 0.075 0.008 TYR C 330 PHE 0.031 0.006 PHE A 383 TRP 0.067 0.011 TRP A 479 HIS 0.007 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.02078 (15230) covalent geometry : angle 1.69371 (20743) SS BOND : bond 0.01516 ( 35) SS BOND : angle 2.69248 ( 70) hydrogen bonds : bond 0.15103 ( 488) hydrogen bonds : angle 6.84082 ( 1287) link_BETA1-4 : bond 0.06976 ( 12) link_BETA1-4 : angle 4.75011 ( 36) link_NAG-ASN : bond 0.07795 ( 45) link_NAG-ASN : angle 3.79042 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 TRP cc_start: 0.8342 (m100) cc_final: 0.7943 (m100) REVERT: C 99 ASN cc_start: 0.8842 (p0) cc_final: 0.8400 (t0) REVERT: C 423 ILE cc_start: 0.9017 (mt) cc_final: 0.8774 (tt) REVERT: C 434 MET cc_start: 0.9039 (ttp) cc_final: 0.8420 (ttp) REVERT: D 586 TYR cc_start: 0.9342 (t80) cc_final: 0.9073 (t80) REVERT: D 601 LYS cc_start: 0.8405 (mttt) cc_final: 0.8028 (mtmt) REVERT: D 604 CYS cc_start: 0.6017 (m) cc_final: 0.5767 (m) REVERT: D 633 LYS cc_start: 0.8162 (mttt) cc_final: 0.7944 (mttp) REVERT: D 659 ASP cc_start: 0.7730 (t0) cc_final: 0.7503 (t0) REVERT: A 53 PHE cc_start: 0.8422 (p90) cc_final: 0.8188 (p90) REVERT: A 69 TRP cc_start: 0.8717 (m100) cc_final: 0.8395 (m100) REVERT: A 320 THR cc_start: 0.9478 (m) cc_final: 0.9268 (p) REVERT: E 210 PHE cc_start: 0.8038 (m-80) cc_final: 0.7817 (m-80) REVERT: F 571 TRP cc_start: 0.8350 (t60) cc_final: 0.7998 (t60) REVERT: F 637 ASN cc_start: 0.8315 (p0) cc_final: 0.7691 (p0) REVERT: F 638 TYR cc_start: 0.8296 (m-80) cc_final: 0.7771 (m-10) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1406 time to fit residues: 70.2921 Evaluate side-chains 171 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 355 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN D 543 ASN B 585 HIS B 640 GLN ** F 540 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 = 0.3752 r_free = 0.3752 target = 0.118377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098395 restraints weight = 31218.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101784 restraints weight = 19930.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104054 restraints weight = 13519.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.104334 restraints weight = 10209.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104739 restraints weight = 9917.480| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15322 Z= 0.174 Angle : 0.769 19.169 20984 Z= 0.371 Chirality : 0.049 0.403 2567 Planarity : 0.004 0.042 2585 Dihedral : 8.620 93.154 3171 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.10 % Allowed : 7.86 % Favored : 90.04 % 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 aren not related in a simple way. whole: 0.22 (0.20), residues: 1616 helix: 1.21 (0.28), residues: 381 sheet: 0.21 (0.23), residues: 415 loop : -0.33 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 166 TYR 0.019 0.002 TYR B 643 PHE 0.033 0.002 PHE F 522 TRP 0.028 0.002 TRP D 614 HIS 0.005 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00378 (15230) covalent geometry : angle 0.70133 (20743) SS BOND : bond 0.00288 ( 35) SS BOND : angle 1.01432 ( 70) hydrogen bonds : bond 0.05177 ( 488) hydrogen bonds : angle 5.64548 ( 1287) link_BETA1-4 : bond 0.00798 ( 12) link_BETA1-4 : angle 3.47320 ( 36) link_NAG-ASN : bond 0.01214 ( 45) link_NAG-ASN : angle 3.54509 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8600 (p0) cc_final: 0.8373 (t0) REVERT: C 475 MET cc_start: 0.8378 (tpp) cc_final: 0.8063 (tpt) REVERT: D 584 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 655 LYS cc_start: 0.8471 (tptt) cc_final: 0.7256 (pttp) REVERT: A 195 ASN cc_start: 0.7533 (t0) cc_final: 0.7214 (t0) REVERT: A 320 THR cc_start: 0.9408 (m) cc_final: 0.9093 (p) REVERT: B 530 MET cc_start: 0.8868 (mtm) cc_final: 0.8400 (mtp) REVERT: B 647 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8072 (mm-30) REVERT: E 376 PHE cc_start: 0.8205 (m-80) cc_final: 0.7927 (m-10) REVERT: F 571 TRP cc_start: 0.8119 (t60) cc_final: 0.7825 (t60) REVERT: F 637 ASN cc_start: 0.7983 (p0) cc_final: 0.7195 (p0) REVERT: F 638 TYR cc_start: 0.7954 (m-80) cc_final: 0.7495 (m-10) REVERT: F 655 LYS cc_start: 0.8713 (tptm) cc_final: 0.8426 (tppt) outliers start: 31 outliers final: 17 residues processed: 223 average time/residue: 0.1273 time to fit residues: 42.1002 Evaluate side-chains 179 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 664 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 63 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 85 optimal weight: 0.0170 chunk 159 optimal weight: 2.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN F 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095273 restraints weight = 31659.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097825 restraints weight = 20445.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099481 restraints weight = 14688.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099792 restraints weight = 12306.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099962 restraints weight = 11448.300| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15322 Z= 0.179 Angle : 0.684 15.974 20984 Z= 0.334 Chirality : 0.047 0.319 2567 Planarity : 0.004 0.041 2585 Dihedral : 6.953 71.680 3171 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.37 % Allowed : 8.88 % Favored : 88.75 % 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 aren not related in a simple way. whole: 0.18 (0.21), residues: 1616 helix: 1.55 (0.28), residues: 374 sheet: 0.07 (0.23), residues: 421 loop : -0.47 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 432 TYR 0.015 0.002 TYR A 486 PHE 0.021 0.002 PHE E 53 TRP 0.021 0.002 TRP C 69 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00406 (15230) covalent geometry : angle 0.62990 (20743) SS BOND : bond 0.00427 ( 35) SS BOND : angle 1.20062 ( 70) hydrogen bonds : bond 0.04549 ( 488) hydrogen bonds : angle 5.24577 ( 1287) link_BETA1-4 : bond 0.00693 ( 12) link_BETA1-4 : angle 2.25460 ( 36) link_NAG-ASN : bond 0.00611 ( 45) link_NAG-ASN : angle 3.11576 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8638 (p0) cc_final: 0.8391 (t0) REVERT: C 154 MET cc_start: 0.8874 (mmm) cc_final: 0.8619 (mtp) REVERT: D 584 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 629 LEU cc_start: 0.8832 (tp) cc_final: 0.8620 (tp) REVERT: D 659 ASP cc_start: 0.7130 (t0) cc_final: 0.6897 (t0) REVERT: A 195 ASN cc_start: 0.7831 (t0) cc_final: 0.7443 (t0) REVERT: A 320 THR cc_start: 0.9417 (m) cc_final: 0.9117 (p) REVERT: B 595 ILE cc_start: 0.9360 (tt) cc_final: 0.9098 (pt) REVERT: B 647 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7865 (mm-30) REVERT: E 376 PHE cc_start: 0.8381 (m-80) cc_final: 0.8133 (m-10) REVERT: F 637 ASN cc_start: 0.8088 (p0) cc_final: 0.7526 (p0) REVERT: F 638 TYR cc_start: 0.8045 (m-80) cc_final: 0.7716 (m-80) REVERT: F 655 LYS cc_start: 0.8776 (tptm) cc_final: 0.8490 (tppt) outliers start: 35 outliers final: 24 residues processed: 201 average time/residue: 0.1210 time to fit residues: 36.3127 Evaluate side-chains 181 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 631 TRP Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 664 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN C 374 HIS D 543 ASN D 651 ASN F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.112867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092700 restraints weight = 31972.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095790 restraints weight = 20384.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097500 restraints weight = 14030.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097699 restraints weight = 11432.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098128 restraints weight = 10751.748| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15322 Z= 0.211 Angle : 0.702 21.761 20984 Z= 0.337 Chirality : 0.047 0.479 2567 Planarity : 0.004 0.048 2585 Dihedral : 6.656 59.866 3171 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.37 % Allowed : 9.89 % Favored : 87.74 % 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 aren not related in a simple way. whole: 0.14 (0.21), residues: 1616 helix: 1.44 (0.28), residues: 380 sheet: 0.09 (0.24), residues: 421 loop : -0.50 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 432 TYR 0.019 0.002 TYR E 40 PHE 0.019 0.002 PHE C 376 TRP 0.057 0.002 TRP F 628 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00487 (15230) covalent geometry : angle 0.63950 (20743) SS BOND : bond 0.00449 ( 35) SS BOND : angle 1.10560 ( 70) hydrogen bonds : bond 0.04485 ( 488) hydrogen bonds : angle 5.23745 ( 1287) link_BETA1-4 : bond 0.00506 ( 12) link_BETA1-4 : angle 1.88228 ( 36) link_NAG-ASN : bond 0.00673 ( 45) link_NAG-ASN : angle 3.50061 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8570 (p0) cc_final: 0.8359 (t0) REVERT: C 106 GLU cc_start: 0.8086 (tp30) cc_final: 0.7753 (tp30) REVERT: C 154 MET cc_start: 0.8894 (mmm) cc_final: 0.8605 (mtp) REVERT: D 584 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 195 ASN cc_start: 0.7912 (t0) cc_final: 0.7503 (t0) REVERT: A 320 THR cc_start: 0.9481 (m) cc_final: 0.9187 (p) REVERT: A 330 TYR cc_start: 0.8276 (p90) cc_final: 0.8012 (p90) REVERT: A 432 ARG cc_start: 0.7195 (ttp-110) cc_final: 0.6531 (ptm-80) REVERT: E 376 PHE cc_start: 0.8530 (m-80) cc_final: 0.8317 (m-10) REVERT: F 581 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8991 (tp) REVERT: F 637 ASN cc_start: 0.7992 (p0) cc_final: 0.7277 (p0) REVERT: F 638 TYR cc_start: 0.8040 (m-80) cc_final: 0.7716 (m-80) REVERT: F 655 LYS cc_start: 0.8866 (tptm) cc_final: 0.8559 (tppt) outliers start: 35 outliers final: 23 residues processed: 190 average time/residue: 0.1230 time to fit residues: 34.7755 Evaluate side-chains 172 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 631 TRP Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 158 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.113748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093706 restraints weight = 31813.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096422 restraints weight = 19381.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098725 restraints weight = 13406.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098894 restraints weight = 10617.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099371 restraints weight = 10233.708| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15322 Z= 0.145 Angle : 0.630 13.851 20984 Z= 0.305 Chirality : 0.047 0.827 2567 Planarity : 0.003 0.042 2585 Dihedral : 6.133 59.288 3171 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.10 % Allowed : 10.57 % Favored : 87.33 % 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 aren not related in a simple way. whole: 0.12 (0.21), residues: 1616 helix: 1.59 (0.28), residues: 382 sheet: 0.05 (0.24), residues: 421 loop : -0.59 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 327 TYR 0.011 0.001 TYR A 486 PHE 0.018 0.002 PHE A 53 TRP 0.041 0.001 TRP C 69 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00331 (15230) covalent geometry : angle 0.57395 (20743) SS BOND : bond 0.00291 ( 35) SS BOND : angle 0.95671 ( 70) hydrogen bonds : bond 0.04092 ( 488) hydrogen bonds : angle 5.02680 ( 1287) link_BETA1-4 : bond 0.00490 ( 12) link_BETA1-4 : angle 1.61065 ( 36) link_NAG-ASN : bond 0.00407 ( 45) link_NAG-ASN : angle 3.15452 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8508 (p0) cc_final: 0.8291 (t0) REVERT: C 106 GLU cc_start: 0.8030 (tp30) cc_final: 0.7668 (tp30) REVERT: D 584 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 107 ASP cc_start: 0.8342 (t0) cc_final: 0.7873 (t0) REVERT: A 195 ASN cc_start: 0.7905 (t0) cc_final: 0.7558 (t0) REVERT: A 320 THR cc_start: 0.9451 (m) cc_final: 0.9185 (p) REVERT: A 330 TYR cc_start: 0.8219 (p90) cc_final: 0.7856 (p90) REVERT: E 315 GLN cc_start: 0.8002 (mp10) cc_final: 0.7461 (mp10) REVERT: F 637 ASN cc_start: 0.7925 (p0) cc_final: 0.7210 (p0) REVERT: F 638 TYR cc_start: 0.8009 (m-80) cc_final: 0.7683 (m-80) REVERT: F 655 LYS cc_start: 0.8877 (tptm) cc_final: 0.8565 (tppt) outliers start: 31 outliers final: 21 residues processed: 193 average time/residue: 0.1225 time to fit residues: 35.6609 Evaluate side-chains 178 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 631 TRP Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 664 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN F 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.109450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089362 restraints weight = 32289.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091649 restraints weight = 21039.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.092966 restraints weight = 15399.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093223 restraints weight = 13432.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093456 restraints weight = 12556.843| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 15322 Z= 0.263 Angle : 0.746 15.657 20984 Z= 0.363 Chirality : 0.050 0.631 2567 Planarity : 0.004 0.052 2585 Dihedral : 6.483 50.495 3171 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.37 % Allowed : 11.59 % Favored : 86.04 % 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 aren not related in a simple way. whole: -0.29 (0.21), residues: 1616 helix: 1.24 (0.27), residues: 382 sheet: -0.29 (0.24), residues: 412 loop : -0.78 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 432 TYR 0.013 0.002 TYR E 40 PHE 0.018 0.003 PHE A 53 TRP 0.032 0.002 TRP C 112 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00615 (15230) covalent geometry : angle 0.69793 (20743) SS BOND : bond 0.00526 ( 35) SS BOND : angle 1.14870 ( 70) hydrogen bonds : bond 0.04815 ( 488) hydrogen bonds : angle 5.29183 ( 1287) link_BETA1-4 : bond 0.00449 ( 12) link_BETA1-4 : angle 1.56984 ( 36) link_NAG-ASN : bond 0.00491 ( 45) link_NAG-ASN : angle 3.21786 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.8058 (mm110) cc_final: 0.7834 (mm-40) REVERT: C 99 ASN cc_start: 0.8575 (p0) cc_final: 0.8299 (t0) REVERT: C 106 GLU cc_start: 0.8181 (tp30) cc_final: 0.7764 (tp30) REVERT: C 425 ASN cc_start: 0.8055 (t0) cc_final: 0.7822 (t0) REVERT: D 584 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 629 LEU cc_start: 0.8758 (tp) cc_final: 0.8501 (tp) REVERT: A 51 THR cc_start: 0.9387 (m) cc_final: 0.9134 (p) REVERT: A 195 ASN cc_start: 0.7994 (t0) cc_final: 0.7513 (t0) REVERT: A 320 THR cc_start: 0.9551 (m) cc_final: 0.9231 (p) REVERT: A 432 ARG cc_start: 0.7220 (ttp-110) cc_final: 0.6529 (ptm-80) REVERT: B 617 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8558 (mtpp) REVERT: E 315 GLN cc_start: 0.8106 (mp10) cc_final: 0.7477 (mp10) REVERT: E 423 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9172 (mp) REVERT: F 588 ARG cc_start: 0.6846 (mmt180) cc_final: 0.6557 (tpp-160) REVERT: F 637 ASN cc_start: 0.7879 (p0) cc_final: 0.6896 (p0) REVERT: F 638 TYR cc_start: 0.8202 (m-80) cc_final: 0.7629 (m-10) REVERT: F 655 LYS cc_start: 0.8857 (tptm) cc_final: 0.8592 (tppt) outliers start: 35 outliers final: 21 residues processed: 184 average time/residue: 0.1226 time to fit residues: 33.1830 Evaluate side-chains 170 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 631 TRP Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 658 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 124 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.111158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.090403 restraints weight = 31889.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093123 restraints weight = 20168.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094970 restraints weight = 14791.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096182 restraints weight = 11901.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097143 restraints weight = 10240.818| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15322 Z= 0.184 Angle : 0.661 16.604 20984 Z= 0.319 Chirality : 0.047 0.665 2567 Planarity : 0.003 0.049 2585 Dihedral : 6.189 50.800 3171 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.69 % Allowed : 13.35 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.21), residues: 1616 helix: 1.37 (0.28), residues: 382 sheet: -0.30 (0.24), residues: 400 loop : -0.76 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 432 TYR 0.014 0.001 TYR C 40 PHE 0.018 0.002 PHE A 53 TRP 0.028 0.001 TRP D 571 HIS 0.004 0.001 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00425 (15230) covalent geometry : angle 0.61368 (20743) SS BOND : bond 0.00343 ( 35) SS BOND : angle 1.04593 ( 70) hydrogen bonds : bond 0.04285 ( 488) hydrogen bonds : angle 5.13279 ( 1287) link_BETA1-4 : bond 0.00413 ( 12) link_BETA1-4 : angle 1.43949 ( 36) link_NAG-ASN : bond 0.00383 ( 45) link_NAG-ASN : angle 2.97335 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7920 (mm110) cc_final: 0.7333 (tt0) REVERT: C 87 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: C 99 ASN cc_start: 0.8522 (p0) cc_final: 0.8289 (t0) REVERT: C 106 GLU cc_start: 0.8107 (tp30) cc_final: 0.7665 (tp30) REVERT: C 377 ASN cc_start: 0.8075 (t0) cc_final: 0.7834 (t0) REVERT: C 425 ASN cc_start: 0.7956 (t0) cc_final: 0.7687 (t0) REVERT: D 584 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7892 (tm-30) REVERT: D 628 TRP cc_start: 0.8948 (m100) cc_final: 0.8738 (m100) REVERT: D 629 LEU cc_start: 0.8710 (tp) cc_final: 0.8406 (tp) REVERT: A 51 THR cc_start: 0.9392 (m) cc_final: 0.9124 (p) REVERT: A 195 ASN cc_start: 0.7988 (t0) cc_final: 0.7569 (t0) REVERT: A 320 THR cc_start: 0.9502 (m) cc_final: 0.9202 (p) REVERT: E 315 GLN cc_start: 0.8036 (mp10) cc_final: 0.7404 (mp10) REVERT: E 423 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9176 (mp) REVERT: F 637 ASN cc_start: 0.7734 (p0) cc_final: 0.6737 (p0) REVERT: F 638 TYR cc_start: 0.8094 (m-80) cc_final: 0.7510 (m-10) REVERT: F 655 LYS cc_start: 0.8933 (tptm) cc_final: 0.8593 (tppt) outliers start: 25 outliers final: 19 residues processed: 176 average time/residue: 0.1263 time to fit residues: 33.3846 Evaluate side-chains 171 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 HIS Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 631 TRP Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 658 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 162 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 157 optimal weight: 0.2980 chunk 136 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 543 ASN F 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.113167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092920 restraints weight = 31932.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096494 restraints weight = 20013.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098598 restraints weight = 13294.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.098936 restraints weight = 10102.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099195 restraints weight = 10047.045| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15322 Z= 0.127 Angle : 0.610 16.184 20984 Z= 0.296 Chirality : 0.045 0.536 2567 Planarity : 0.003 0.057 2585 Dihedral : 5.825 50.665 3171 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.90 % Allowed : 13.35 % Favored : 84.76 % 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 aren not related in a simple way. whole: -0.11 (0.21), residues: 1616 helix: 1.56 (0.28), residues: 383 sheet: -0.25 (0.24), residues: 413 loop : -0.72 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.011 0.001 TYR C 40 PHE 0.018 0.002 PHE A 53 TRP 0.030 0.001 TRP D 571 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00289 (15230) covalent geometry : angle 0.56774 (20743) SS BOND : bond 0.00260 ( 35) SS BOND : angle 0.89754 ( 70) hydrogen bonds : bond 0.03847 ( 488) hydrogen bonds : angle 4.93543 ( 1287) link_BETA1-4 : bond 0.00434 ( 12) link_BETA1-4 : angle 1.36662 ( 36) link_NAG-ASN : bond 0.00380 ( 45) link_NAG-ASN : angle 2.72336 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7917 (mm110) cc_final: 0.7376 (tt0) REVERT: C 99 ASN cc_start: 0.8480 (p0) cc_final: 0.8248 (t0) REVERT: C 104 MET cc_start: 0.8886 (ttm) cc_final: 0.8498 (ttt) REVERT: C 106 GLU cc_start: 0.8080 (tp30) cc_final: 0.7685 (tp30) REVERT: C 377 ASN cc_start: 0.8011 (t0) cc_final: 0.7803 (t0) REVERT: D 584 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 51 THR cc_start: 0.9374 (m) cc_final: 0.9089 (p) REVERT: A 195 ASN cc_start: 0.7954 (t0) cc_final: 0.7598 (t0) REVERT: A 320 THR cc_start: 0.9443 (m) cc_final: 0.9180 (p) REVERT: E 315 GLN cc_start: 0.7999 (mp10) cc_final: 0.7385 (mp10) REVERT: E 423 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9107 (mp) REVERT: F 655 LYS cc_start: 0.8903 (tptm) cc_final: 0.8683 (tppt) REVERT: F 657 GLU cc_start: 0.8386 (tp30) cc_final: 0.8166 (tp30) outliers start: 28 outliers final: 19 residues processed: 191 average time/residue: 0.1252 time to fit residues: 35.9849 Evaluate side-chains 176 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 HIS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 631 TRP Chi-restraints excluded: chain F residue 645 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 8 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 377 ASN F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.113262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092365 restraints weight = 31595.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095302 restraints weight = 19276.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097240 restraints weight = 13817.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098693 restraints weight = 11002.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099555 restraints weight = 9244.997| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15322 Z= 0.131 Angle : 0.632 16.486 20984 Z= 0.305 Chirality : 0.045 0.528 2567 Planarity : 0.003 0.043 2585 Dihedral : 5.796 59.371 3171 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.56 % Allowed : 13.96 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.21), residues: 1616 helix: 1.63 (0.28), residues: 383 sheet: -0.21 (0.24), residues: 411 loop : -0.75 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 327 TYR 0.012 0.001 TYR A 486 PHE 0.017 0.002 PHE A 53 TRP 0.030 0.001 TRP D 571 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00299 (15230) covalent geometry : angle 0.58056 (20743) SS BOND : bond 0.00258 ( 35) SS BOND : angle 1.09145 ( 70) hydrogen bonds : bond 0.03779 ( 488) hydrogen bonds : angle 4.88157 ( 1287) link_BETA1-4 : bond 0.00430 ( 12) link_BETA1-4 : angle 1.33786 ( 36) link_NAG-ASN : bond 0.00384 ( 45) link_NAG-ASN : angle 3.04205 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8514 (p0) cc_final: 0.8291 (t0) REVERT: C 106 GLU cc_start: 0.8076 (tp30) cc_final: 0.7659 (tp30) REVERT: C 180 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8172 (m-30) REVERT: D 584 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7839 (tm-30) REVERT: D 626 MET cc_start: 0.7485 (ttt) cc_final: 0.6991 (ttt) REVERT: D 633 LYS cc_start: 0.8327 (tppt) cc_final: 0.8125 (mttm) REVERT: D 634 GLU cc_start: 0.6957 (pm20) cc_final: 0.6562 (pm20) REVERT: A 51 THR cc_start: 0.9362 (m) cc_final: 0.9083 (p) REVERT: A 195 ASN cc_start: 0.7922 (t0) cc_final: 0.7575 (t0) REVERT: E 125 LEU cc_start: 0.9576 (mm) cc_final: 0.9367 (mt) REVERT: E 315 GLN cc_start: 0.7944 (mp10) cc_final: 0.7378 (mp10) REVERT: E 423 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9163 (mp) REVERT: F 530 MET cc_start: 0.8290 (mtp) cc_final: 0.7981 (mmt) REVERT: F 638 TYR cc_start: 0.7977 (m-80) cc_final: 0.7656 (m-10) REVERT: F 655 LYS cc_start: 0.8961 (tptm) cc_final: 0.8686 (tppt) REVERT: F 657 GLU cc_start: 0.8343 (tp30) cc_final: 0.8129 (tp30) outliers start: 23 outliers final: 19 residues processed: 178 average time/residue: 0.1305 time to fit residues: 34.4989 Evaluate side-chains 175 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 631 TRP Chi-restraints excluded: chain F residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 543 ASN F 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.111652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091571 restraints weight = 31878.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094394 restraints weight = 19645.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096715 restraints weight = 13339.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096978 restraints weight = 10360.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097231 restraints weight = 9727.314| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15322 Z= 0.174 Angle : 0.656 16.760 20984 Z= 0.319 Chirality : 0.046 0.532 2567 Planarity : 0.004 0.048 2585 Dihedral : 5.846 50.173 3171 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 1.42 % Allowed : 14.63 % Favored : 83.94 % 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 aren not related in a simple way. whole: -0.18 (0.21), residues: 1616 helix: 1.58 (0.28), residues: 384 sheet: -0.22 (0.24), residues: 416 loop : -0.87 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.013 0.001 TYR A 486 PHE 0.016 0.002 PHE A 53 TRP 0.031 0.002 TRP D 571 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00408 (15230) covalent geometry : angle 0.61199 (20743) SS BOND : bond 0.00356 ( 35) SS BOND : angle 1.05010 ( 70) hydrogen bonds : bond 0.04074 ( 488) hydrogen bonds : angle 4.93361 ( 1287) link_BETA1-4 : bond 0.00376 ( 12) link_BETA1-4 : angle 1.32567 ( 36) link_NAG-ASN : bond 0.00378 ( 45) link_NAG-ASN : angle 2.86818 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8535 (p0) cc_final: 0.8279 (t0) REVERT: C 106 GLU cc_start: 0.8091 (tp30) cc_final: 0.7687 (tp30) REVERT: C 180 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: D 584 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7852 (tm-30) REVERT: D 634 GLU cc_start: 0.6937 (pm20) cc_final: 0.6511 (pm20) REVERT: A 51 THR cc_start: 0.9348 (m) cc_final: 0.9092 (p) REVERT: A 195 ASN cc_start: 0.7997 (t0) cc_final: 0.7653 (t0) REVERT: E 125 LEU cc_start: 0.9587 (mm) cc_final: 0.9387 (mt) REVERT: E 315 GLN cc_start: 0.7946 (mp10) cc_final: 0.7401 (mp10) REVERT: E 423 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9217 (mp) REVERT: F 530 MET cc_start: 0.8199 (mtp) cc_final: 0.7962 (mmt) REVERT: F 638 TYR cc_start: 0.8088 (m-80) cc_final: 0.7766 (m-10) REVERT: F 655 LYS cc_start: 0.9015 (tptm) cc_final: 0.8716 (tppt) REVERT: F 657 GLU cc_start: 0.8362 (tp30) cc_final: 0.8143 (tp30) outliers start: 21 outliers final: 17 residues processed: 167 average time/residue: 0.1195 time to fit residues: 29.7083 Evaluate side-chains 168 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 631 TRP Chi-restraints excluded: chain F residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 125 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 377 ASN F 543 ASN F 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089856 restraints weight = 31861.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093339 restraints weight = 19991.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094650 restraints weight = 12801.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095105 restraints weight = 11139.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095405 restraints weight = 10416.718| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15322 Z= 0.233 Angle : 0.702 16.648 20984 Z= 0.343 Chirality : 0.048 0.564 2567 Planarity : 0.004 0.043 2585 Dihedral : 6.158 49.889 3171 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.69 % Allowed : 14.50 % Favored : 83.81 % 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 aren not related in a simple way. whole: -0.40 (0.21), residues: 1616 helix: 1.38 (0.28), residues: 388 sheet: -0.42 (0.24), residues: 416 loop : -0.97 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 327 TYR 0.016 0.002 TYR B 643 PHE 0.017 0.002 PHE C 376 TRP 0.029 0.002 TRP D 571 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00545 (15230) covalent geometry : angle 0.66034 (20743) SS BOND : bond 0.00442 ( 35) SS BOND : angle 1.12456 ( 70) hydrogen bonds : bond 0.04454 ( 488) hydrogen bonds : angle 5.05588 ( 1287) link_BETA1-4 : bond 0.00359 ( 12) link_BETA1-4 : angle 1.33541 ( 36) link_NAG-ASN : bond 0.00391 ( 45) link_NAG-ASN : angle 2.89978 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2293.21 seconds wall clock time: 40 minutes 42.50 seconds (2442.50 seconds total)